I also use 2 Colortunes - but on my 6 cylinder (2 carbs) I put them on #1 and #6 on the assumption that minimizes the effect of the 2nd carb on each reading. No idea if that assumption is valid.
As noted, syncing the carbs is a whole 'nother process and must be done before the mixture is adjusted. The balancing (or syncing) of the carbs is more of a mechanical adjustment than a tuning issue, thus it can be done on a cold engine, no need to wait until it is warmed up. In fact - if you could connect a huge electric motor to the engine and spin it you could sync the carbs -- as all you are doing is balancing the air pulled in by the intake strokes.
I use a Uni-Syn though some use a hose and do it by ear. You can even use a homemade manometer. If I were buying a tool for this today I would consider a gauge type tool (Air Flow Meter) just because it looks easy to read with some precision.
FWIW - mixture is one of the last steps when I tune. Generally it goes: valve adjustment, points gap, timing, new or clean plugs, sync, mixture and idle speed.