You don't need to unlink the codes. You should just be able to turn them off in the IR screen in sage.
But first question first...are you using a usb-uirt? Because right now thats the only one xlobby can handle natively. The use of a different ir reciever would require girder. LovingHD has some experience with that I think. He's still here so I'm hoping he got it worked out.
You want XLobby and Sage to both load on startup. XLobby on top of Sage.
Here's a writeup I did over at Sage...
IF YOU DO NOT HAVE IR SETUP AT ALL...
-Copy the 'ir' folder from XLobbyMC.zip into your XLobby directory (often 'c:\program files\xlobby')
-Allow it to overwrite...this will replace you existing XLobby ir commands with a template to learn against using a usb-uirt and remote of your choice.
-Open XLobby and press 'F2' to enter setup
-Goto the 'IR Plugin' tab.
-Make sure 'IR Plugin' is set to USB-UIRT
-Under 'Device' choose (xlobby) xlobby-xlobby-xlobby instead of (c) c-c-c.
-Hopefully you have lots of commands in the list box now.
-To learn commands from your remote...
.....click a command
.....click 'Set' next to ID:
.....push the button on your remote you want to assign
.....click 'Learn'
.....hold down the button on your remote you want to learn till it reaches 100%
-There you go command learned!
Command Definitions (for those that are not obvious)
-Exit (SageTV back button...I suppose I should call it Back)
-Menu (Sends XLobby to Main Menu and gives XLobby focus..works in XLobby and Sage)
-My TV (sends Sage to My TV screen and gives Sage focus...works in XLobby and Sage)
-Next / Previous are the FF2/RW2
-Settings (In XLobby goes to Settings screen, in Sage goes to Sage Settings screen)
-Commands that have dual/triple function will work differently in different parts of XLobby. If you start a movie in ZP 'Next' skips chapters. If you're listening to music, 'Next' is next song, if your're in Sage it's whatever FF2 is for you.
That should cover IR commands I think...
let me know if that does it for you
oh and minimizing is fine, when you kick the ir codes in i find that the only time I ever see the sage main menu is when a tv show ends, since the menu button on the remote is setup to goto xlobby's menu but shouldn't actually need to minimize it, you just don't want it bringing up that screensaver ontop of xlobby. I use sendfocus which you have to put at c:\ to switch between the two programs. When in sage an you push menu it brings xlobby to the front and when you select the 'my tv' button it brings sage to the front and sends it to the 'my tv' screen.