First, load the Logic (or Cubase / Cakewalk) config with the Shift-F1 combination.
Press EZ Routing, F1-F4 On/Off, F1 (in). This shows your virtual patch bay with the physical inputs on the top and the computer tracks on the bottom. Change #1 to say Ch01=In09, routing the RCA left to the computer input Ch01. Use the cursor keys to change all inputs as desired. These settings will save automatically until the next time you load a configuration.