Hi @Colby Wallace,
I'm a designer working at Cadre Design, an architecture firm in Manayunk. It's difficult to give an exact answer without knowing the specifics of your project, but here are some general rules that apply to (almost) all zoning types in Philly.
Any mid-block lot has to have 30% open area in total. This means that a 50' lot needs to have a 15' rear yard. There is no by-right exception to this, but if all your neighbors have smaller rear yards, you can appeal for a variance and it usually goes through (but I'm not a zoning lawyer so don't take my word for it).
Corner lots must have 20% open area in total. The city actually likes for you to build closer to this limit. They like the visual look of a more filled-in block with larger buildings capping the end of the street.
There are requirements for a minimum rear yard (9' required) regardless of lot depth, which means that if you have a really small lot you can end up with less than 70% coverage (typical Philly trinity styles rowhomes).
On the subject of 3rd floor setback, I'll need to look up the specific code, but other than RM-2 or greater, or CMX-2 or greater, the height of your front facade will be limited to what your neighbors are doing.
So if you have 2-story neighbors on both sides, your front facade will be limited to 2-stories after which you'll need an 8' setback for the 3rd floor. If you have a vacant lot on one side, you have no setback requirement. If one of the two houses has a 3-story facade, you have no setback requirement.
I use these guides (provided by the city) as a quick reference. They're reworking the CMX guides right now, so they've taken those guides down for now. Hopefully this is helpful. Feel free to reach out if you have any questions.
http://www.phila.gov/CityPlanning/projectreviews/P...
http://phillyzoning.com/newcode/wp-content/uploads...