well the lower the ohms the less resistance...so it would be more efficient...but 1000w rms @2 ohms is the same as 1000w rms @4ohms. its just the resistance of the speaker. 2 ohms puts less strain on your battery and alternator. don't quote me on this but 4 ohms might have better sq than 2 ohms...
2 ohms puts more strain on your battery than 4 ohms, given the same amp, given two different amps, one that does 1000W at 2 ohms, and the other doing it at 4 ohms, the 2 ohm will draw less current. 4 ohms does have better SQ, more headroom, more damping, you're straining the power supply less.
You can hook up to 2 ohms if you want (or if possible) but if you can wire the subs for a 4 ohm bridge, it would be better than a 2 ohm load on each channel because the signal would be in mono. Really, the amp shouldn't pull a whole lot more current when running a 2 ohm load, but with inefficiency and heat, it can tend to do so a tad more.
my personal view? if you can afford it, give the subs full power from an amp running a 4 ohm load. a 4 ohm load will yield less heat and distortion, better SNR, and damping than an amp at 2 ohms. The drawback is that you'll pay a lot more for an amp that puts out 500 watts at 4 ohms versus 500 watts at 2 ohms.
The reason people run amplifiers at 2 ohms is to squeeze more power out of them. It's a 'cheaper' way to get more power, at the price of sound quality.