I made a new Compiler in Build Settings -> Compilers. I've added the compiler and linker in the Tools section, and modified the File Types section to work with the new compiler.
The problem that I ran into is that I need a non standard build command for the new linker. It seems to be hard coded into CodeLite and so any linker that doesn't use the exact same build command as GCC's linker just won't work.
This is the hardcoded format that I found in the auto generated Makefile.
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$(LinkerName) $(OutputSwitch)$(OutputFile) @$(ObjectsFileList) $(LibPath) $(Libs) $(LinkOptions)
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$(LinkerName) @$(ObjectsFileList), $(OutputSwitch)$(OutputFile),, $(LibPath) $(Libs) $(LinkOptions)