Be sure the framing is level before adding the joists.
How to level a roof deck.
We used a water level which is clear tubing connected to the ends of a garden hose.
When you start installing the posts for your deck you will need to make sure that each one is plumb.
In whatever manner a deck is constructed over a roof maintenance for cleaning and repairs of the membrane below is recommended.
Mount one end on a corner of the rim then check the height of the water to level the other corners.
Once it s level nail the brackets to the rim joists.
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There are proprietary pedestal systems that provide a very stable level and serviceable deck over a roof membrane though they are relatively expensive compared to conventional methods.
Check and plumb two adjacent sides.
You can use the same rubber roofing material by cutting it to contour it to the size of the problem area then bonding it to the roof with bitumen.
Another tool that can be used is a plumb bob.