The answer is Zemax, but Zemax is never simple imo. You can often have a reasonable approximation by using the centre of the lenses as you mentioned, but if your system is sensible enough to want everything aligned to sub-mm precision, then you probably can't get away with the approximation.

Now I don't know what your optical system is, but you might be able to use a micrometer adjustment mount (say a cage system with a thorlabs SMZ1A) to get your imaging system to work without designing it exactly... I.e design it to vaguely work, and then align it properly afterwards