The factorization of $N$ is useful, since $$(a^2+b^2)(c^2+d^2)=(ac+bd)^2+(ad-bc)^2$$ There are good algorithms for expressing a prime as a sum of two squares or, what amounts to the same thing, finding a square root of minus one modulo $p$. See, e.g., http://www.emis.de/journals/AMEN/2005/030308-1.pdf
Edit: Perhaps I should add a word about solving $x^2\equiv-1\pmod p$. If $a$ is a quadratic non-residue (mod $p$) then we can take $x\equiv a^{(p-1)/4}\pmod p$. In practice, you can find a quadratic non-residue pretty quickly by just trying small numbers in turn, or trying (pseudo-)random numbers.