So to boil down your question, you're asking if you can rank a range of combos vs another range of hands; the very short answer is no you can't. The only software I know that can do this is exactly is StoxEV. However, constructing a scenario in sEV takes minutes rather than seconds like in combonator; i think it's much quicker to just construct the range manually.
Longer answer: There are tools in combonator to make close approximations; plus often doing simple x% vs a range is not really what you want to do anyway.
I'm going to paste in a much longer response i sent via email to a user who asked a similar question. It's a common question and one that deserves a decent answer.
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Range vs range isn't supported; i want to add it, but it's a bit tricky to add whilst keeping the program fast. However, though range vs range by equity for range construction would be cool, it's not necessary and in many cases, and might not be what's desired; building up a range manually is often more representative, and it only takes about 10-15 seconds to do.
Now it definitely would be nice to do 'top 80% vs my preflop opening range of 40%', for sure, and for that you need Cardrunners EV right now.
But, what you can do instead is do top 80% vs some weak made hand. In your example, top 80% by equity vs 32o (BPBK) produces:
This looks really close to what a sensible continuing range might be; all pairs and Ax, gutshots, flush draws, folding the weaker Kx, Qx.
(there's one anomaly here, A3o and K3o, and that's because we're up against 32o; so we need to add these 2 in manually; It's certainly a bit of a 'hack' and it would be better if we could do this vs an actual range rather than some kind of weak pair, for sure)
The other alternative is to build up the 80% naturally using the auto-selectors, and imo this produces the best results - because pure showdown equity does not represent well good continuing hands (we need to account for hands with good implied odds vs those with RIO, hands with semibluff equity on future streets etc, playability etc...).
So instead of thinking 'my opp will continue with hands based on equity', you take the more natural approach of 'my opponent is going to continue with all hands of value, hands with draws, bluff catchers'.
So here, I start by adding 50% by pure hand value, then all flushdraws, then all gutshots, then all backdoor straights + backdoor flushes (i did them in separate groups just to demonstrate, but this can all be added into the same group):
(This sounds like a lot of work, but really it takes about 10 seconds once you are familiar with the program.)
This is 75% of the range. So then i might manually add in manually a combo here or there to bring this up to 80%; i added in A5o, A4o, and the remaining combos of A5s and A4o to get 80.2%.