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Justin,
Code Composer Studio (CCS) v3.3 and v4.x both should be able to be succesfully installed on a single PC. CCSv3.3 does not have to be uninstalled before installing CCSv4.x. However; the two versions of the program should not be run at the same time to avoid hardware permission conflicts.
The version of CCSv4.1.1 that is bundled with the TMS570 MDK or TMS570/470M USB Stick Kit(s) is intended to be used with these evaulation kits only while using the on board XDS100v2 JTAG emulator. It is not intended to be used with other MCU boards or other JTAG emulators (like the XDS510USB). If another board is built by a customer and an emulator other than an XDS100v2 is used a different license of CCSv4.x needs to be purchased.