On cards like the yavaris title, can I use a token to pay its cost or does it have to be the dial. Also, the book says if you usr a card, the normal command dosent take effect. So if I use it, I cant move and shoot with some ships and let others double tap their shots correct?

It doesn't "cost" a command to use it. Whenever you resolve the effect of that command (either a token or a dial) the upgrade card's effect happens as well.

A token and a dial both resolve the command. Unless a card specifies one or the other, either or both can be used.

The command still goes off normally unless the card specifically says otherwise (i.e. Nav Team gives you the choice of yaw instead of changing speed).

The command symbol followed by text just means "Whenever you resolve this command, the following happens:"

For Yavaris, it's

[When you resolve a Squadron command]: Each squadron you activate can attack twice if it does not move.

Emphasis mine to clarify the point. When you are resolving a squadron command, each squadron that you activate can choose to attack twice if it does not move. So yes, some may double-tap while others move and shoot (or shoot and move).

was going to type a post detailing this, but, ya....what Joker said