I think that we should be able to have mulitple sets of parents if you've marked one set as your adopted parents. As people use these kinds of sites more and more to find out who their biological parents are, those people should be able to list both sets of parents.
If you are working with FTB this can be done with the options provided, for I have done it. The person will appear in the tree twice, because of the two different relationships, but that can be taken care of with a note. I don't know if this is possible with an on-line only tree. Also check the HELP manual; there may be another solution there.