So, did a few cycles of 5/3/1 and this week decided to give The Juggernaut Method a try. My training since starting 5/3/1 has looked like this; wake up, take the dog for a walk for some NEPA, lift somewhere between nine and one, depending on class and work that day and follow it immediately with conditioning (prowler, tire flips, etc).
I've heard there are some benefits to dividing your training up into two separate sessions, however, everything I've read seems to make it sound like this works best for strength sessions. Is there any benefit to doing your conditioning work at a separate time? Aside from resting and getting some energy back prior; or lack of time to do it at once.
Yes there is. And actually, the two reasons you mentioned are a lot more substantial than you might think. Conditioning is, much like strength work, first and foremost a question of sustained, hard effort. The results depend primarily on the amount of effort you can drive into your session. If you're exhausted before you go to your conditioning work, how effective do you think that conditioning work is going to be? Answer: not at all. Better than nothing, but not by much.
Most forms of conditioning are focused on maintaining a high intensity of work for a period of time. Power-endurance, or strength-endurance, anaerobic conditioning (working in an oxygen debt). Endurance is fine, but it is only half the purpose of conditioning. If endurance were the only thing that mattered then we wouldn't need any other form of conditioning work than log jogs, runs, or bikes. It would defeat the purpose of HIIT and strongman style training for conditioning work.
In general, it is always better to split up your work sessions. This is true for pretty much everything, not just strength. Thibaudeau has written about this subject, as have other coaches. There as always certain exceptions, but they are just that: exceptions. The biggest exception would be if you were intentionally trying to do more work in a very fatigued state, which is sometimes a goal for certain athletes.
It generally leads to a bigger metabolic boost to separate your sessions. Also, it keeps you from bastardizing your workouts to try to hit everything at once: you stay focused on your One Big Goal, not getting distracted by a bunch of different goals.