For the average person it's easier to leave the front shaft installed and don't install the belt. Be sure to put a bolt in the hole where the front bshaft belt tensioner pulley was installed or you'll have a masive oil leak.
For the rear, replace the bshaft with the stubby shaft. If you are swapping over your pump that already has this done, there is nothing more to do.
On the subject of reusing oil pums, are you sure this is one worth reusing? Did you have a real oil pressure guage on th previous motor to get some readings? I just ask because it is too much work to do twice. Although with no rear bshaft it can be done with the motor in the car with rlative ease at least.
Hopfully something in there answered your question.