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Because drain fittings use somewhat flexible washers... either rubber or plastic... to seal the joints, there is some allowance for "crookedness" in the connections. However, there is a point where seepage will occur so it may be wise to try to straighten them as much as possible.
In my experience, one of the biggest mistakes made by do-it-yourselfers when cutting drain pipe under sinks is either cutting the pipes too long or cutting them too short. Overly long pipes will force the trap assembly out of alignment and put unnecessary stress on all connections.
Cutting the pipes too short can be a silent killer... even though the connection seems water tight, over time leaks can start. A good knock with a bottle of mouthwash can cause a too-short tailpiece (the vertical pipe beneath the strainer) to dislodge from the trap, leading to a disastrous leak! A good rule of thumb is to cut the pipe so that at least an inch of pipe extends beyond the connection's washer. You'll get plenty of strength with no binding.
You didn't say whether or not you are trying to work with old or new parts. My suggestion is that IF you are trying to stop a leak it is usually better to purchase new parts once you get the assembly apart than to reuse the old ones. The only exception would be if the drain assembly is fairly new and corrosion-free.
There are some special-situation plastic drainpipes that are designed to "flex" so you have a little more wiggle room if the original plumbing is out of whack! One of these might help you get things back into "whack"!
As a final suggestion, when assembling a sink drain, always keep all connections threaded but loosely fit until you have all parts properly aligned. Then begin to tighten them. A small amount of plumber's grease on the threads only will make tightening a little more effortless and more effective.