I'm getting full fiber installed in my house, and when it is am I still able to put my router anywhere in the house?
You will have to connect the hub to the ONT.
Can i ask the enginner to install the ONT upstairs on the second floor in my office as that is where my router is?
You can ask. Normally they will be helpful.
We had two days of engineers recently (long story) both sets said they needed to minimise time in the house and would need to install ONT in the house as close to the CSP as possible to avoid long cable runs. Luckily for us this was perfect position.