Yep, the OP is putting his handiwork at risk doing his piping before the footer is dug. Even with staked flags showing their location, it will make it harder for the footer to get dug by a back hoe if there are too many pipes installed beforehand. Not the normal chain of work progression... for sure....
Normally.... Just dig and pour the footer, lay or pour the foundation walls, grade the floor space dirt, install the rock inside the foundation...then the plumber does his under ground piping and pipe stub ups in the rock for the slab prep pour. The owner or plumber usually sleeves or most of the time, just hand digs under the footer later for the main sewer pipe exit. JMO