Doors first, then the biggest flat points on the car. Can do wonders with modeling an 5% coverage, but without fancy math and a ton of time (ie the OE's have a hard time doing it) 25% coverage is a good approximation with only a little more weight.
If you were to go with rich00's recommendation of 2 12's on 2k here's just a quick search on ssa's store of budget friendly (using the $1000 you listed) and is good quality.
2 american bass xfl 12's (177 ea) $354
American bass ph4000 amp $260
Sky high ofc 0ga amp kit $115
Total: $729
And this set up should be able to slam.
Just to show your $1000 budget is very doable.