firstly if your fitting these it's easier and better to remove the engine, the time taken to do this will save you a lot of hassle later on.
Fuel out/inlets, I took my fuel line (as you look into the engine bay) to the upper left and then ran a line from the lower left to the upper right the lower right needs blanking (small hose with blot in it in you have to).
The brass vaccum take offs are there for balancing the carbs as long as these are in, you do not need to do anything with them, it however is advisable to remove these before you install the engine as the snap easy (yes I done it).
When fitting the manifolds you will also need to ease the tin work a bit around the inlet area unless you have better manifolds than mine.
Also make sure that the choke controls on the side of the carbs is blanked off unless your running sp fan shroud as this gets in the way also.
Make sure before you go though this heart ache that the carbs are atleast a matched set (same internals and chokes etc).
I will say that once fitted it does make a difference to response/economy etc, we are running 40's on a stock 16 tp, I know it's a bit over the top but they were bought in readiness for a CC upgrade.