I can speak about my only front line type (Jaguar) which will follow similar principles to most other FJs.
To allow fuel in you have to de-pressurise the tanks just as you would on the ground. Obviously as the tanks fill you need somewhere for the air to escape to as the fluid goes in. This will mean the aircraft is transferring fuel via gravity feed. This is fine since you will almost certainly be in 1G flight. Once the tanks are full the engine will then provide bleed air to pressurise the tanks to force fuel through in all flight regimes.
The tanks in the Jaguar would kind of fill up in reverse order to how they emptied. Most FJs aren't as sensitive to CofG as you might think. If they are they tend to have a clever system to automate the process.
I hope that answers your question. I'm sure some people cleverer than me will be along shortly to elucidate further.
BV
