wildehond,
The easiest example is alwaays single span, no end restraints uncracked. So that is what they put in books.
You can model the PT as equivalent loads to try to work out the Mp. Then subtract P.e from this to get the Secondary prestress moments so Msec = Mp - P.e.
In your ultimate load case, the combination would then be
1.2DL + 1.6LL + 1.0 Msec.
I hope you were not putting in Mp for this because as Hokie66 says, the main prestress moment is an internal action, not an external load. The only effect of the prestress that is considered to be an external load is the secondary moments.
Some designers agree that this should have a .9 factor (RAPT software allows this but it defaiults to the code value) but most codes use 1.0. There is a theory that it is actually zero at ultimate strength as after the plastic hinges form, there should be no secondary moments as there is no continuity!
As long as you consider the stress concentrations from the applied loads, then FEM is ok. It is not concervative, it is correct.
The ACI code method is unconservative. Many designers using FEM for PT design still take averages over the full slab width. This is useless. FEM is predicting the concentrations and the designer is ignoring them after going to the trouble of calculating them. Also, if the concentrations are ignored some funny things can start to happen, e.g.
1 when people average the moments in irregular buildings, often they are averaging across a zone that has both negative and positive moments. Theoretically, if the negatives equal the positives, the result is zero! Not very sensible as both moments exist.
2 If you are designing for a one way failure mechanism, as the US method does, you cannot analyse for it on FEM as it is considering 2way action. The torsions and effects of stiff elements from different areas of the slab affect the moments in the area you are designing and can lead to stupid results and gross underdesign (similer to 1 above).
3 You cannot average effects across a change in section (eg drop panels)