I just want to double check and see if I am using the proper tokens for the right purposes.

The arc-shaped numbers I presume to be used to identify ships when using multiples of the same ships. One goes on the ship (on the base) and one goes beside the ship card. However, there is also a oval-shaped number --- what is that for? How about the oval-shaped Rebel and Imperial tokens (lower right)? Or the arc-shaped Rebel and Imperial tokens (upper right)?

They're double sided flagship markers. The ovals go on the cards, the arcs are in the ship holders (The black and white facings indicate to which 'side'/player the ship belongs) .

I own the X -Com game, and I use an X Com token to mark my flagship.

The oval goes on your ship card. You get 2 of the other numbers (1 light, 1 dark) to mark your ships and to provide a contrast for red v red matches at tourneys.

I own the X -Com game, and I use an X Com token to mark my flagship.

I may have to do this.

Thanks guys!