How do I nail plywood to flat roof framing?
First concideration, I would encourage you to use a T&amp;G roof sheathing such as AdvanTec instead of standard CDX plywood. This will give you a better fit and not have to worry about spacing gaps in the plywood. The price is comparable, so there is no cost advantage to using regular plywood. 

The sheathing should be secured with 6d galv ring shank nails at apx 8" spacing. 1 5/8" coated drywall screws are great, but more time consuming to install. Don't use non galv common nails, as they tend to back out after a few years.

If your sheathing fits properly on the joists with 3/4" overlay, nailing straight down is fine as long as you bite into solid wood. A slight angle towards the joist is OK  as long as the heads of the nails or screws don't protrude above the sheathing. Protruding nails can damage your roofing material, assuming you are not planning on using a layer of Grace Ice and Water shield under your final roofing materials.