I misread that. I thought they were 500w each.
If you're dead set on wanting to use 3 subs:
1000w is 1000w whether its from one amp or two. There's no risk to your alternator or any electrical, as long as you use cable that is "at least big enough".
Your alternator recharges the battery. If you draw more than it can recharge, then you're just going to watch your voltage gauge slowly drop, until it eventually kills the battery (which will take a while). All you have to do is turn the volume down. If you set it up as two amps, you just pull the fuse out of probably the 12" until you upgrade the alt.
WHAT I WOULD DO: Go ahead and set up both amps. Run it, see how it effects your electrical, and then disconnect the 12" and see how much of a difference it makes. THEN REEVALUATE whether or not a 3rd sub and an upgraded alt is worth it. You might barely notice the bump, and it's about 40 amps, which on a stock alt with where this is going, might be the difference in needing a new alt or not. Price out the alts, see if it's worth it. If you built the box, maybe you have spare wood, and want to try a different design with two, or maybe you can modify that one to add ports.
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