I think drilling was necessary in the old P3 (pre 2013), but with the current model going internal is easy. The battery simply goes in the seat tube and you can put the junction box in a bento box or just tuck it under the stem.

Ah cool. Does the SM-JC41 junction box go in the seat tube or down tube?

Any place it will fit.

Wherever is most convenient considering your frame and wire lengths.
Consider that you want the most slack on the wire from the B junction to the battery, so seat tube gives you a little more length if you have it to spare from the cable running from the stem (A junction).

Thanks for the tips.

I am sure this will be clearer to me once I have the frame and components in front of me!

Before you begin install, connect just the battery to the A junction box to your computer and let it charge. Then, update the FW. (Some systems, it is important to update the battery first before anything else.)
Then, connect the other bits and update their FW, check operation, tweak settings, etc.

Once everything is up to date and verified in working order, put the wires up against your bike and check lengths. You need a little slack around the stem so they don't pull out when turning. You need as much slack at the seat post/battery, so that you can remove the seat post without pulling out the cable. Hopefully, all the wires are long enough. If you're a weight weenie, you'd consider rebuying any that are too long.

Once everything is figured out, install away!

Thanks. The kit I have ordered doesn't include wires so I will work out what lengths I need.

I weigh 95 kg so the weight of an overly long wire isn't going to make much difference :-)