There are specialists in this kind of thing, and I am not one of them. But let me say a few things that may help.
First, if the degree of the polynomial is not too big, or if the prime is not too big, the problems are surmountable. I don’t know how I would attack a degree-$1000$ polynomial over $\Bbb F_{1009}$, however, though I might try these tricks:
You certainly want to look for roots. If you’re not in a mood to try all the elements of $\Bbb F_p$, you can try finding the gcd of your polynomial with the polynomial $x^p-x$, because this is the product of all polynomials of form $x-a$ with $a\in\Bbb F_p$. If the gcd is not $1$, it will be the product of all the monic linears, so you really have the roots in hand.
Similarly, if there are no roots, then you might look at $(x^{p^2}-x)/(x^p-x)$. This is the product of all the irreducible monic quadratic polynomials over $\Bbb F_p$. Again, take the gcd of this with your original polynomial, and again, if the gcd is not $1$, then it will be the product of all quadratic factors of your polynomial. You might try this with a random quartic over $\Bbb F_p$ for a prime that’s not too large, and see how it works out.