Well you could do it that way, If I have understood your description correctly.
However, taking your exhaust as the example as it is most clearly visible in your pic' I suggest screwing both the pipes 'in' to meet at the midpoint of the central block. This is done first 'away from the field of battle' as a preparatory gambit. . This will temporarily make the overall length of the connecting pipes as short as possible.
Then drop that assembly in line with your cylinders. This may involve some (very gentle!!) wiggling and juggling.
Additional note: You can if you wish drop this exhaust pipework into position before both the cylinders are fitted. In this case the total overall width of the pipework can be the distance between the outside of your frames. This approach may be easier to get the pipework into place BUT it will mean that you will need to remove (or at least loosen) one of the cylinders if you wish to remove the pipework at any time in the future. This can be a royal pain! As thread starts are unlikely to align exactly it can make initial cylinder thread engagement awkward too. Though looseness in thread engagement normally allows for this.
Anyway, to return to the main drama:
Having got your pipework roughly in place and your cylinders secured: Unscrew one of the exhaust pipes from the central block whilst holding the central block 'in place' (i.e. 'centrally'!) and keeping the outlet vertical. As the pipe is 'unscrewed' from the central block it will engage with and 'screw-into' the cylinder on that side. When you have 'adequate' engagement of this thread at both the cylinder and central block – stop. Now tackle the other pipe connection: supporting the central block (and keeping the outlet vertical) unscrew this pipe in turn, once again, as it unscrews it will engage with the thread in the cylinder and screw-in. Some gently 'joggling' may be required to start the thread, there should be enough 'give' to allow this. Once again when 'happy' with the engagement on this side – stop. The exhaust pipework should now be self-supporting – but lock-nuts (gently applied) can assist.
If you have a go I'm sure that it will become clear. Basically your start-point is to make the overall width of the pipework as long as possible when screwed fully into the central connector whilst still allowing it to be joggled into position between the frames. Martin Evans will have calculated this for you in the dimensions and extent of threading that he has stipulated. Unscrewing each horizontal pipe in turn from this central connector engages the relevant pipe with the cylinder.
Your exhaust will be low-pressure so easier to deal with. Once you have established how the system works you follow the same principle with the inlet – which of course is high pressure so will almost certainly need a dab of your preferred jointing.
Be gentle when screwing your pipework in and out – indeed 'gently does it' is the watch-word at every stage right from the beginning of the procedure – keep in mind that you are dealing with soft copper so easy to deform and damage the thread! (I could tell you how I know – but you can almost certainly guess. At least it is quick and easy to make-up new pipes tho'.)
Good luck!
Phil