First understand that trying to do everything at one is a recipe for disaster. The body has a limited capacity to handle stress.
Regarding condtioning, I would do it at th e end of regular sessions using a fairly novel way of training: non-lactic acid conditioning.
Pick your comnditioning exercises, either as a circuit or done by themselves Give yourself a specific time frame (e.g. 15 minutes). Within that time frame you must strive to do as much work as possible BUT NEVER LET LACTIC ACID ACCUMULATE. As soon as you feel a hint of burning stop and rest just enough to be able to resume the work without accumulating lactic acid.
As for hypertrophy work, I'd do it either between sets of the main exercises or at the end. But I would be VERY careful to avoid doing too much. Only consider adding hypertrophy work for muscles that might be neglected by the main lifts.