If she's trading her Baron title away, you don't get two landmasses to combine, you get either a town or city (whichever you choose). She gives up her settlement with her title.
If she keeps her title, then you have separate settlements.
Towns and strongholds are pre-placed. The only way you can combine them is by building one from scratch nearby, and hope the Duke is willing to help pay for that stronghold. Remember, a military baron signs a contract with the duke to pay for the stronghold and the garrison.
If you want to build a castle in your city, you can do that, but the duke probably won't pay for it. It will be very expensive.
If you want to build a city around your castle, it may be subject to siege and a lot of damage, and make it harder to defend.