well lets see BNSF has a mainline that basically terminates at 19th ave and w. mcdowell rd in phoenix,az. it also is where the engine service and storage tracks are they have a interchange track for dropping off/picking up freight cars with Union Pacific at it's yard that from memory I believe starts about 7th ave below madison ave.
Union Pacific most of its freight trains uses a cutoff about 30 miles south of the metro phoenix area and heads to Gila Bend,Az and heads to California. last I knew there are a few freight trains that do come to the Union Pacific yard in phoenix,az they and BNSF do have switching crews dropping off and picking up freight cars.
as to freight trains running straight thru phoenix not to my knowledge. BNSF has a large and just expanded inter-modal yard off grand ave between w. bethany home rd and goes south to w. camelback rd. above bethany home rd is a large holding yard for the double stacks and mixed freight cars heading out of town and also mixed freight originates in phoenix area.
BNSF has a large auto unloading yard off grand ave in El Mirage,az, it used to be near the inter model-yard but they moved out some time ago to the above location.