1. Salaries and Contracts can be entered onto the CBS site. No problem. Commish can enter that info when he puts in the rosters. Also handles max in season team salaries and contract years.
2. Never dealt with minor leagues. They do have slots for minor League Players though on their options screen so I would assume they handle it fine. Also, anyone in the system can be added as a reserve and CBS has a database of players that looks like it includes the 40 man rosters of the MLB teams if not more. So drafting and holding in that regard should not pose too much of a difficulty.
3. Never played CBS in a H2h format, so I simply do not know. Only deal with Roto.