so when it's 1v1 each player has 2 fleets, do these fleets have to remain totally separate or can i use say, an interdictor from one fleet to fill out the other?

Those Two Fleets are completely Separate Entities.

So although you may use the same Interdictor model in each fleet, they are counted as 2 Separate Ships...

And it wouldn't be a problem unless you wanted to do an All-Out Battle at the end........ And needed both Interdictors at the same time.