These are the stock parts that you will take out, all the ends on the wall are the top.

You shouldn't have to remove the rubber boots on the top of rear springs with your OME kit.
I installed a Dobinsons kit and the top of the rear springs are tighter then the standard springs, the rubber boots didn't fit in the new springs.
Top of standard rear springs.

Top of Dobinsons rear springs.

As Scrawn said, it's pretty simple just take note of how they come out and make sure the bottom of the spring seats into the plate properly.