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Yes your right, but if you want more space it's either that or going down to the one sub and amp. If your worried about the amp being too big for the one sub, sell it and get a smaller amp or go to an audio shop and get it tuned properly to the one sub. you just wont be getting the most out of the amp that you could be getting, thats all.
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that amp is fine for one and both subs. 400w at 4 ohm for the one and 800w at 2 ohm for the two of them so its not much over their RMS ratings. Just keep the LPF around 45-60hz and the input/gain at around half. no need to change or buy anything new