David,
From a CCS standpoint there is not a necessarily preferred directory to install it. The major difference is if you intend to install it as a regular user (which will require additional steps at the end to install the device drivers) or as root.
If installing as user, just be sure to run a script at the end to properly install the emulation device drivers.
If installing as root but running as user, just be aware that the lib directory of all compiler tools are by default non-writable for regular users. This causes problem if your project requires to build on-the-fly one of the runtime libraries - check this thread for details. Another more obvious issue is if you intend to install any updates to CCS - you must run as superuser to be able to do so.
I am unaware if there is a preferred install directory for the MCSDK, but you may want to ask it in the multicore forum.
To invoke CCS from the command line just run /<CCS_INSTALL_DIR>/ccsv5/eclipse/ccstudio &
(the last ampersand is to release the terminal after the command runs)
Hope this helps,
Rafael