When I was at Newport we ran one of 3 routes:
1) The 1.5 mile on the road along the river on flat pavement
2) A 2.2 mile run that went on roads throughout the base and included some hills
3) A 5K that went to the 'seawall' and back. This was only ran twice. They said it was a "at your own pace" run, but the DIs still provided motivation.
M/W/F/Sat are run days, in that you will do one of the above during PT. But that is not the only exercise you will do that day. Your morning will start with the typical workout and will still include plenty of pushups, situps, and whatever other calisthenics your DI likes (mine liked lunges and bear crawling, while another loved 8-count bodybuilders). You will also often get stopped in the middle of the run to do suicide sprints and other calisthenics.
Tues/Thurs are more creative "strenght and conditioning" exercises instead of the runs. You'll do things like deadman carries and caterpillar walks. One DI had a former sports trainer in his class, so he had that guy set up an obstacle course. It's really DI choice on these days, and often they don't happen if your class is supporting graduation practice.
On a run day it will look something like this:
-Muster in formation 0520. Stretch on your own for 10 minutes.
-Commence 1/4 mile-ish formation jog warmup that takes about 2 minutes
-Get in formation for warmup calisthenics. This takes about 10 minutes. You mostly do pushups instead of the warmup exercises, though.
-Do another 1/4 mile-ish warmup lap that takes another 2-3 minutes.
-Break off into your run groups by speed, each led by a staff member.
-Do the run (about 30 minutes, depending on group and how much the DI wants to stop that day).
-Another 1/4 mile cooldown jog for 2 minutes.
-Do suicide sprints or bear crawl until the slow groups are back if you're in a fast group.
-Do cooldown stretches in formation (again, mostly more pushups and leglifts).
-March off for chow.