If you installed Windows 7 with BIOS set to AHCI and have not changed the default storage driver, msahci.sys, then you do not need to run optimizer or even install Toolbox if you have the TRIM firmware installed. Of course, you could use the Toolbox to check SMART and diagnostic work.
If you installed Windows 7 with a different storage driver, then you would need to run optimizer for TRIM--but you need TRIM firmware installed. There will be an updated firmware release in the future that will negate the need to run optimizer with storage drivers other than the default msahci in Windows 7.
There is no need to reinstall the OS as far as I can see from your posting.
After I install the new SSD Optimizer, will it know which files are actually deleted already?
Yes it will. While trim will only clean up after new deletes. One exception being files left in the recycle bin. These will be trimmed when the bin is emptied.