Gnat, I might have misinterpreted your question about the combining of the two rca outputs on your stereo into a single rca input on your amp, but:
If you have one input on your amp, then its a mono amplifier (or single-channel amplifier) designed to supply a signal to a single output channel, for example, your single subwoofer.
If there are two rca outputs on the back of the stereo deck, then the deck is designed to be able to run either a stereo amplifier (ie two-channel amplifier) or two single-channel amplifiers. There is nothing wrong with bridging the two stereo RCA outputs together into a single rca cable to connect to your mono-channel amplifier. You can use a two-female to single-male adapter. This will not damage your stereo or your amplifier. RCA cables only carry a cold signal, there is no "heat" to the signal like there is in speaker wires. You can't bridge speaker wires together into a mono signal the same way.
Hopefully this makes sense...