One note... The ConnectIQ SDK doesn't support any platforms other than MacOS and Windows (no Linux support). If you insist on it, you'll likely be able to get some of it to work, but I don't think anyone will make any guarantees.
How familiar are you with unix platforms? Have you checked the permissions on the monkeyc and monkeydo scripts (use ls -l ~/connectiq/bin/monkey{c,do} and check for the execute bit in the appropriate location)? If the files are executable, can you invoke them by explicitly specifying the path to the script (use ~/connectiq/bin/monkeyc to verify you can invoke the compiler). If this works, then it is likely that ~/connectiq/bin is not in your PATH (if bash is your shell, you can export PATH=$PATH:~/connectiq/bin to add it to your path temporarily, or you can add that line to your startup scripts to do it more permanently).
