I'm in the same boat, I was planning on working on FTP a little bit before Boston just for whatever head start I can get and then just shifting to serious FTP focus after Boston.

If you are in pretty good bike shape now, it is unlikely you will get in better bike shape while training for a marathon.

"increasing FTP" just means getting in better bike shape, there is nothing specific you do to accomplish it other than ride your bike a lot.

Best bet would probably be to do zone2 rides with whatever spare time you have, after the marathon bike fitness will come on very quickly.

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Kat Hunter reports on the San Dimas Stage Race from inside the GC winning team
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Freelance sports & outdoors writer Kathryn Hunter

This pretty much says it all.

What kind of running mileage are you planning to do? I did a marathon last year, and found I had quite a lot of spare training time and energy over and above the run training, simply because my "engine" is capable of a lot more volume and intensity than my legs are when it comes to running. Assume if you're BQ then you're at a higher level than me, but I was maxing out at ~40mpw (i.e. <6 hours) so had enough time to maintain my cycling fitness as well. I did all my running in the mornings, which meant I could do cycling training in the evening as and when I felt like I could do so without impacting the next day's run.

My running week typically looked like:

Monday - medium run with intervals/speed/threshold/hill work
Tuesday - recovery run
Wednesday - medium run with intervals/speed/threshold/hill work
Thursday - recovery
Friday - off
Saturday - long run
Sunday - recovery

I'd typically fit in 2-3 cycling sessions on top of that. Thursday evening I could go hard (something like 2 x 20') as I would be fairly fresh with no hard work scheduled the next day. Then Tuesdays and Fridays I'd normally get just try and get a couple of hours in the saddle, normally from commuting, and would go as hard or easy as I felt like depending on freshness.

I did a 100 mile bike event a couple of months after the marathon, so ramped up the volume and actually found I was in pretty good cycling shape.

Serious run training will get you in decent bike shape on its own. And as for Jack's comment about zone 2... I don't know if that's the best use of time when you're already on a marathon training plan. Running 60-80 mpw (conservatively) eats up time. 3+ hour zone 2 rides eat up time, and don't really benefit running or pure cycling fitness on top of the base running miles you'll be doing. I'd go more for replacing a 6-8 mile recovery run with 3x20 or 2x30 at 95% FTP (I think that's zone 4, but will depend on what system you're using). You'll get the long slog, "strength" miles into your legs with the running shoes on.

Now, if you have nothing but time on your hands (no family, no job, etc...) Go out and ride 2-3 hrs a day at 60-70%. You'll still have time to run and recover.

"I would like to increase my FTP over the winter but I'm afraid I would lose it once I ramp up running."

When are you planning on "ramping up" the running? For a mid-April marathon, you would probably want to start in December at the latest, and ramping up the mileage while doing a lot of hard bike workouts is likely to result in injury.

If I were you and Boston was a priority, I would start increasing the run load today (if you aren't currently running 6+ X/week, I'd work towards that) and find a good 24 week program to start in a few weeks. I've had good results following one of Pfitzinger's programs from his book, there are various programs for different levels of fitness. Bike when it works for you, even 2-3X week for an hour or two.

I did this (focused on running) for several winters, with varying amounts of biking. Even in the winter where I stopped biking completely for 4 months, 6 weeks after I resumed bike workouts I was setting PRs on the bike while maintaining the significant running gains I'd seen during the 4 month running focus.

This is kind of my approach but I'm not terribly concerned with where my biking will be after Boston. Sitting on 75mpw currently and building to 100mpw; riding will consist of hour long work commutes a couple times a week and that's pretty much it, maybe a two hour zone 2ish ride on the weekends as well.

Why would you do 3x20 at 95% if you're supposed to do a recovery run?

3 reasons:

1) You're looking to actively improve FTP while training for a marathon
2) Cycling is non-impact, and you can recover much easier from a hard ride than a hard run. You may have a little fatigue in the legs, but there's little injury concern when riding compared to running.
3) Running requires more work, so total energy expenditure for a recovery run will be similar to an FTP-style workout on the bike.
e.g.: For me to run 7 min miles for an hour (13.8 kph - 3.83 m/s) I use roughly 1035 kJ
That same energy expenditure on the bike will put me at 287 W average over that hour. If my FTP is 300, that's right about 95%
(As a rule of thumb, running speed in m/s = cycling power in W/kg)

I run about 3-4 marathons per year and still try to fold in quality triathlon training (especially cycling). I don't have all the answers but when I ramp up for a hard marathon effort ("easy" marathon efforts are a different story for me) I like to do only a couple of cycling workouts per week but try to do them hard. Like, 1 hour each at .90 or greater IF. For me, it helped keep my FTP up and didn't impact my next day's run too badly. Granted, I wouldn't go and do running intervals the next day after the hard cycling session. YMMV but thought I'd share my approach. Good luck!

Not sure if you've ran Boston before (I did in 2011) but if not, be sure to take the time and enjoy it. What a great place, great race, etc.

#1 got me. Had moved past the FTP idea.

When you're doing a couple hard run efforts a week on top of some serious long runs with marathon pace work thrown in, your body may simply not have much in it to do a lot of riding. Listen to your body, and definitely don't tank your quality runs by doing hard cycling intervals the day before a quality run workout. I've reached my 60+ mpw phase in training for the Honolulu Marathon and I'm weary to throw much more at my body except a couple easy rides a week, not doing huge volume, and maaaaybe one day of intervals on the bike per week. So long as I can mostly maintain the FTP I've built up this year, I'll be happy and can make some big gains January-April on the bike.

Also, ask yourself what your ultimate goal for Boston is. If you want to smash a PR, then any interval work on the bike is going to be wasted effort and negatively impact your recovery from your quality run workouts. If you just want to finish Boston feeling good, then you can certainly spend some quality time on the bike as well and make some FTP gains.