This works by changing only the entries in your specx640.lst files in your Ivfiles directories, it does not change or move the OPT files themselves. 
(The specx320.lst files are not changed so these can be used as backups.)

If you have BoP you will have the option of making the changes to the XvT.lst files too.

To use the OPT File Manager, select a ship slot from the left column, (the OPT file entry currently in the specx640.lst is shown at the bottom of the box,) then select the OPT file you want to assign to that slot from the column on the right, and press the Assign button. 

An * next to the ship slot indicates a non-default OPT is assigned to that slot. To restore the default OPT for that ship slot, press Restore.

Where the buttons are deactivated, the ship slot is not functional.

The column on the right will open to your preferred OPT directory as defined in Preferences. It must be XWingTie\Ivfiles, BalanceOfPower\Ivfiles, or one of their subdirectories.  For convenience, I'd recommend making a folder (e.g.Custom) within your ivfiles folder where you put all your custom OPTs and install them from there.

It seems that the SAT/1 and SAT/2 slots are both assigned to the same OPT, so are effectively the same slot. The same goes for NAVs and PROBES.

You may also rename the selected Ship Slot by typing in a new name and pressing the Rename button. This only changes the name in the list within XvtED (by altering the Ships.txt file) for easier reference while mission building.