in order to be able to answer your first question: "how to get the damn things to lign up correctly" we would need some sort of picture showing what you've got... I realise you don't currently have the possibility of showing one but i think updating this post once you are able to shouldn't be a problem. to answer your second question reguarding fuel flow, the transfer stage of all my interplanetary bound modules has very little fuel, in fact it can only take 4 tons from low kerbin orbit to duna 100km orbit so i employ an extra orange tank for anything heavier... fuel does automatically crossfeed from it to the transfer stage and it drains from the extra tank first