There is no easy way to compare matches.
I created a database using Bento (cost $50!) and manually copied and pasted all matches (99% to Low) for myself and my Mom. I also enter all new matches including very low ones. This has been a great help. I can now search my database before analyzing a match. If it also matches Mom, I know to look on her side. If not, it's my dad's side. In a few instances, we both match but my match is stronger. This tells me it's a match for both sides.
You could do the same thing in another database like Access or in Excel. With Excel, I'm always fearful that I'll accidentally disassociate data by not highlighting all columns.
I can't wait until ancestry has improved search capabilities. In the meantime, my makeshift database has been a godsend.