With regard to the MOD FSCTE (Fire Training) at Manston, the closure of the airfield should have no impact on them (now re-named as the Defence Fire Training and Development Centre) as the RAF camp is separated from the airfield by a public road and was retained by the MOD when the RAF airfield was sold.
The only thing they wouldn't be able to do is fly any airframe in to Manston for transfer to the RAF side (such as the Nimrod). Tornado ZA398 has been moved closer to the B2050 pubic road and I would hazard a guess that it will be taken over to the RAF camp very soon, off the airfield.
Of concern must be the fate of the two aviation museums on the airfield land. The RAF Manston History Museum has many large exhibits such as complete Jaguar, T-33, Wessex, Whirlwind, Chipmunk and Iskra, as well as cockpits of Tornado, Victor, S360 and Buccaneer. The nearby located Spitfire and Hurricane Memorial houses one of each of those types.