I will try to answer (with my limited experience)...
Best practice is to use gridlines to accurately input the column positions.
This accuracy will also help later if you want to do a architectural overlay for cross-checking.
It is also good for setting up gridline elevations later which you can use to easily view bending moments, shear forces etc. along a certain section of the structure.
Columns, beams, walls, slabs, etc. are all modelled based on their centerline positions. If needed, you can apply centerline offsets later on inside the properties for specific members.
Your example of the perimeter beams is one where I would probably ignore offsetting the beam to match the architectural drawings. I think the effect of the offset on the loading mechanisms/transfer to the column may be quite small/negligible... but I could be wrong here. Would welcome the input of others!
-------------
Ilyas