Before I start buying gear I thought I'd run this by the experts here:

I've narrowed down my sonar choices for a remotely operated survey robot to the Garmin EchoMap Plus 40 series because of its 4 wire transducer. Virtually every other sonar on the market uses at least 6 wires (and most are 8 or 9 wires) which is more than my robot can accommodate. According to Garmin's documentation, their EchoMap Plus 40 series uses a 4 wire transducer (for temp, chirp and down scan sonar) and can send NMEA 0183 data (SDDPT and SDDBT sentences) for depth information. I also plan on using a separate GLONASS GPS that will send NMEA 0183 GPS data (RMC sentences) which should be accurate to 3 meters or less. I'm hoping to use a multiplexer to mix these two signals and feed it into my PC running RM. On paper this all should work, or am I missing something?

Yes, you could multiplex them and have them come into RM on one channel, in which case make sure that the sonar unit isn't also sending position data (you will be fine if you limit output to the messages you have specified). Alternatively, you could run position and depth in on two separate channels, which RM can support. You'd just need one extra Serial->USB adapter. Probably better to just pick one depth sentence as well, in case the values within conflict with each other due to unit settings. You can always apply a transducer offset later within RM if required.

Awesome, thanks Matt for the quick reply.