Different lengths usually correspond to different resistances, more resistance the longer it is, and the best solution for this has the least resistance. However, these are minute resistances, usually a few milliohms at the most, so you really dont even need to think about them. (You cannot get much better at all without spending a LOT of money, and it wouldnt be anything near practical)) If you are nervous, check the longer wires with a multimeter to make sure they arent too resistive.
I would personally simply run the largest gauge wire I could, or double the wire up, but it really shouldn't be needed.
As far as somewhat different lengths, on my own projects (as opposed to anything I might sell, ever) I get lazy and do not even really measure wires, so no two wires are the same length exactly.