Indicating co-PI status on a paper
Actually, I've never seen a paper where co-principal investigators (with respect to a grant) have been distinguished—and I was co-advised as a graduate student in exactly such a circumstance.

However, I don't think this is as big a problem as you think. If you were a co-PI, you would indicate the corresponding grant as part of your CV, as well as the resulting publications. So it shouldn't be too hard to figure out who contributed what.

Also, in my own circumstance, I am actively co-advising several students at the moment. In these collaborations, we assign the "senior author" position to the most "relevant" author for the publication. For instance, I'm in engineering and one of my collaborators is in CS. When we publish in a CS venue, he's the senior author; when we publish in an engineering venue, I'm the senior author.

If it's really important, though, to indicate the co-PI issue, you could mention this in the acknowledgments section, since that's where you'd list the grant support in any case. You could write something like


  F.O.O. and B.A.R. were co-principal investigators on grant XYZ from funding agency ABC.


or whatever comparable wording satisfies your needs as well as those of the funding agencies.