Will this affect my saves.

I'll try to keep this simple. I've got Steam installed after installing FM'09 on it. I installed FM'10, but it didn't give me the option of installing via Steam. So I've got FM'10 installed, but not with Steam. I went to Steam then 'Activate a Product on Steam'. Entered my code and it then said 'Do you want to install FM'10?' If I cliked this I wasn't sure if it will re-install the whole game again, and will my current save still be on the game if I click this?

PS: Don't know if this helps but a month or two ago I put FM'10 in my Steam thingy as 'Add a non-Steam game'.

I don't know but you can always back up your save by moving the save game file located at My Documents\Sports Interactive\Football Manager 2010\games to, say, the desktop.

Generally files in the "Documents" folder are left alone during (un)installation, but just back them up somewhere else to be safe.