hi smatticus,
to make piSNES the default simply edit the “es_systems.cfg” file and spot the Super Nes section. Amend it like this:
<system>
<fullname>Super Nintendo</fullname>
<name>snes</name>
<path>~/RetroPie/roms/snes</path>
<extension>.smc .sfc .fig .swc .SMC .SFC .FIG .SWC .zip .ZIP</extension>
<command>/opt/retropie/emulators/pisnes/snes9x %ROM%</command>
<platform>snes</platform>
<theme>snes</theme>
</system>
hope this helps.
cheers,