Nice choice in speakers there fuzz. I think you'll be very happy with the bass output of the Phil3's for both music and movies but if you've got a bit of a sweet spot for bass and need that extra low end for movies, you might find DIY is the way to go.
I think the $1k range for a sub is sort of in an awkward price range. On one hand, you could afford 2 decent commercial subs like the SVS PB12, Rythmik Audio FV12, Cadence CSX12, HSU VTF-1, etc, which I imagine will give you a decent Home Theater experience but on the other hand, however, if you can find it in you to purchase some used gear or wait for a good deal on Amazon, ebay, craigslist, etc, you could get something along the lines of a couple of JL 12w7's (I see them go for 300-400 quite often) and a Behringer EP4000 to power them. An EQ like the DCX2496 would put you over the $1k mark but you may want one eventually. Because the Phil3's will play so low already, I feel like if you want a good chance at improving the bass for around your budget, you'll have to try something a little more extreme like the JL W7 series subs or the single LMS-18 Ultra mentioned earlier (either one of these would get you some unbelievable bass).
Good luck!