Upgrading the applications is about the only alternative.
Both Lion and Mountain Lion have dropped Rosetta which translates PowerPC code to Intel so that the old PPC appilcations could still run then on Intel Maac. Now without Rosetta, you get the errror message when you attempt to execute PowerPC code.
Aatrix Top Pay 17's website indicates that it is an adjunct to Quickbooks for the Mac.
Intuit, the publisher of Quickbooks, has treated the Macintosh like the black sheep of the family, which I know well, as a long time Quicken user (I also had occasion to use Quickbooks for the Mac a decade ago).
However, in a surprising move, Intuit did rewrite and release last March Quicken 2007 for Lion (which is now updated for Mountain Lion). No such luck for Quickbooks...
So you should contact Aatrix and see if they plan to release an Intel version of Top Pay. If not, or until they do, here is the solution that I used to continue to operate my older version of Quicken. This solution will allow you to use Aatrix Top Pay as well concurrently with Mountain Lion, by installing Snow Leopard (with Rosetta) into Parallels:
[click on image to enlarge]
Full Snow Leopard installation instructions are located here: