It is possible to cover all bonuses fully (if you have included the right players). I find I get the best results if I build my sessions like I would build a real life training, including balancing intensity. Play around with it a bit and you'll quickly get the hang of it.
I don't train my bench apart from my main team, I just look at condition. I even train my GK's with the rest of the team, although I'm still not sure if that's wise.
As for starting each training with warm-up: you would be training the same set of skills in every training. I'm not sure if that's a good idea in the long term. I'd rather try to use each drill as much as any other.