No, not quite. You compile to cxi, inject header, and then package the completed work as a cia.
Here's an example from my scripts, based on those used in the ExInjector thread. Mind you, theirs are entirely automated, so I really do advise on trying theirs out if you're a bit lost. This example also packs a manual with the name "manual.cfa" into the cia file.
Code:
cd workdir..\makerom -f cxi -rsf cia.rsf -target t -desc app:4 -v -icon icon.bin -banner banner.bin -exefslogo -code code.bin -exheader decrypted_exheader.bin -romfs decrypted_romfs.bin -o ConvertMe.cxi
cd workdir..\exinjector -rom ConvertMe.CXI -exheader decrypted_exheader.bin -sd
cd workdir..\makerom -f cia -target t -content ConvertMe.CXI:0:0 -content manual.cfa -o Install.cia