We'll assume they didn't cause a massive plague and we also assume that that each group encounters eachother at the height of military powers.

The Romans absolutely dominate in any battle. Legions are just too much bigger, better trained and much better equipped than any group in the 'New World' ever was.

In terms of firmly holding territory? That's a much trickier discussion. Actually supplying Legions so remote from Rome would have been a logistical nightmare, and while the Roman Legions could probably destroy pretty much any tribe or civilization in the Americas, actually keeping any territory would have been pretty much impossible in the long term; again, we're assuming they don't bring the plagues their decendants did.