Hi Tereza,
If the AOI cover different products, you should process them separately and then remove the phase bias between the products on the overlapping area. Preferably you could define a reference point in that overlapping area to get things easier.
My suggestion is to get the orbit which cover all your AOI (if exists). It is less time consuming.
I believe until now no software is ready for what you are looking for.
If this for an exercise or for a something more automatic processing?
Good luck!