I'm not really sure, one strategy that can help is to try and make some areas smooth before filleting since edges that are smooth to each other will have fillets that match each other end-to-end instead of having corner juncture patches needed as when filleting edges that meet at a sharp corner. Another thing that can help in general is to try fusing some smooth pieces together into single faces to reduce the number of edges involved.

But it's a pretty difficult thing to work around, it's far easier to import your object into OnShape and fillet it there, that's what I would recommend.

- Michael