Yeah, two batteries will work fine.
When you're looking at the 4 batteries in the HET, the 2 negative terminals on the right side of both of the right 2 batteries are the ground. The 2 positive terminals on the left side of the left 2 batteries are the 24v positive. The remaining 4 posts in the middle across all batteries are all 12v positive. This can be kinda confusing until you get the hang of it, because you can read positive voltage from a negative terminal.
Basically, in any automotive series or series/parallel battery arrangement, there are 3 possible terminals - 24v positive, 12v positive, or ground. If they're set up the following way, once you identify the 24v positive and the ground terminals, everything else is 12v positive.
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This should be about how the stock HET is setup -
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And this is about what it should look like with only two batteries instead of four -
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