Hi Martin,
It doesn't get complicated as this, you must be having a ball. Anyway this is what I would do.
First check and verify with the stake holders about any possible modules on HR, the final implementation should really consider what else will be implemented so that it can aid reporting, workflows, payroll, ess/mss etc.
Practicalities. Its best to stick to one pernr per employee regardless on what position they are covering. So have as many positions necessary but each position should always be 100% and not more. For cross reporting ie Q4 create a custom relationship which will be maintained for everyone who is doing the BACk to BACK. That way you can report on it
I hope this helps
Dimtri