I train quite a lot on the TT-bike, also on the trainer, but not always. I think my FTP on the TT-bike when in position is about 10watts lower.
What is the best way to handle this in trainer road, as I can not currently setup two bikes with different FTP?
I’m using adaptive training at the monent and the FTP is currently set as according to a ramp test on the road bike.
I don’t think there is a good solution built into TrainerRoad. Except maybe use your referral bonus to reduce the cost of a 2nd account. 
I’ve actually submitted this question to the podcast.
At the moment I’m doing all my rides on TT bike in TT position 
I have a vague memory that they have actually discussed this in the podcast, but I couldn’t find which episode.
Just manually change the FTP according to which bike you’re using.
Found an answer from TR themself: 
This was fine before adaptive training but I’m worried about the effect on the progression levels if I’m altering intensity or FTP
I do all my indoors training on the TT bike and most outdoors training on it too except for winter when I use my road bike so I just accept it 
I’ve been worried about that as well. But what I can understand, the progression is based on how you manage your workouts, in accordance to your FTP.
I think it will be a lot worse and influence your progression more incorrectly if you just leave your FTP to high (or low) and fail (or overachieve) the workout
Guessing that to set a different FTP for the workout will be the same as having two bikes with different FTP’s setup in the system, which is the feature I was hoping for in the first place
Manually changing your FTP is going to play hell with AT. Every time your FTP changes, your PLs will change (the current experience is this is inverse to how your FTP moves. So FTP down, PLs up; FTP up, PLs down).
At the moment if you want to use AT, you are going to have to pick which FTP you are going to use, and stick with that.
This is my concern, it might not be as bad as I fear but for now I’ve done my ramp test on my TT bike in TT position and will do my workouts like that.
I think adjusting your FTP is going to mess with the progression levels as it thinks you’ve gotten stronger or weaker so will want to slide the progression levels accordingly (in theory if you are a 4.0 for threshold and move FTP up, you’re probably a little less than 4.0 in that category at the new FTP).
I’d guess you could consider doing each workout with the intensity slider (100% +- on bottom left) adjusted to what your perceived “bike” ftp adjustment is and maybe have better success than editing your FTP, but even this may be a problem.
I read in a thread somewhere on the forum that AT doesn’t take adjustments to intensity into account when determining your progression levels so that seems like a better choice to me
That is good if true 
Have you thought about splitting the difference. Given that your power meters are likely +/-2% then 5W is probably going to be neither here nor there in terms of training effect.
I can’t speak for the OP but my difference between TT and road FTP is nearer 10% than 10w. Enough to make sweet spot feel like threshold and to make vo2 impossible.
I’m happy enough doing all my training in TT position for now but would be interested to see what trainerroads supported solution would be.
The interesting question is: if you tested FTP via lactate, would you actually have two different FTPs? Or is this more of a positional limitation where your TT position is limiting your ability to produce power / recruit muscle/ breathe?
Interesting in the regard of ”what limits your FTP between bikes”.
But does it really matter in the regard of adaptions and calculations in TR adaptive training?
True! Probably the best work around
When I say I have two "FTP"s I really just mean that I have two different numbers on which to base my workouts.
I know I only have one real FTP and that’s my road bike one… because it’s bigger 