I think you could do this in quicken.

I use quicken for Mac, and unfortunately, Quicken thinks in terms of accounts. I think in terms of purpose. At one investment company I have an account that is mostly intended as college savings (to supplement the kids' 529s), but there is a mutual fund that is NOT part of the college savings.

In Quicken, I download transactions and then drag them from the account they were downloaded into to the account I want them in.

Oh....another thought: in Quicken, I can look at accounts, and I can look at groups of accounts. Quicken aggregates the separate account data from my 3 credit cards into "Credit Cards." I can look at accounts separately or together, as I see fit.