Yes, cats can be trained to sit. The key to this is finding a treat they really like and will work for. Then, use the treat to lure the cat into a seated position whilst using the command "Sit."
This depends a lot on the cat's personality. Some previously outdoor cats actually prefer to be indoor cats as they feel more secure. The trick is to provide ample opportunity...
A truly feral cat is unlikely to adapt well to an indoor life. A feral cat is uncomfortable with human company and may well feel trapped and be very unhappy....
Leave a regular bowl available to give your cat some alternative when first introducing the fountain. Start with the fountain turned off so the cat learns to drink from it...