It is difficult to have both manual and automatic on the same car - I'll grant you that!
If you're asking whether propshafts are interchangeable between manual and automatic, they are. I'm pretty sure the prop shafts are identical between different engines as well - ie diesel, 4 & 6 cylinder petrols. However, the prop shaft is split into 2 pieces with a viscous coupling unit (VCU) splitting them. The diesel & 4 cyl are interchangeable, the V6 is supposedly different - but I don't know by how much and whether they are actually interchangeable - I hazard a guess to say they are.
However, you're biggest question is whether your car is in a condition to allow the props to be reinstalled. The props were removed for a reason! It may just have been noisy support bearings or the owner noticed the VCU beginning to go tight, or the owner wanted to use mismatching tyres - in which case you are fine to reinstall props assuming you have 4 matching (make & model) tyres and the VCU being used is servicable (I would not trust a 2nd hand VCU).
If the owner ran mismatched tyres or an overly tight VCU and then noticed problems - you may just blow your transmission by reinstalling props.
There are some threads on here that discuss reinstalling props and what to look for and test - a search should find them.