I'm pretty sure that you solve it in relatively the normal way. Normally, you end up with a rational number solution to a linear system. Well, over integers, modulo some number, the number in the denominator is not actually divided by in the usual way, but let's say the denominator is d, then you would find the integer q such that d*q=1 mod (whatever), and instead of dividing by d as you would in a linear system over the real numbers, over the integers modulo whatever, you would then multiply by q. The one thing to watch out for, is that if d and whatever (I should have given it a variable letter darnit) have a common factor, if they aren't relatively prime, then there will be no solution for q. But that's nothing new, that's just a new way for the determinant to be 0. So if the determinant of the matrix describing your linear relation is not just 0 as it is with linear systems over all real numbers, but any integer which has any factor in common with "whatever", then you can't solve it.
Now, if you want to solve it where each line in the linear system is modulo a different number, for instance x+3y=4 mod 5, and 2x-y=2 mod 6, then that method isn't going to work. And if it is a nonlinear equation, that is NP complete, so you'd best avoid trying unless you have a polynomial time algorithm for NP problems.