The only time I try not to die is Nebula mission, or when I know I'll have time to regen a few sets of shields to full strength.
orzelek has already covered deep strikes... I believe that you're free to go four hops from player or neutral territory without triggering a particular response.
Two things to be wary of: freeing lots of guard units for threat, particularly in a mark IV system next to your friend's homeworld; setting off a Raid Engine. I'd recommend your friend unlock miniforts or put up a handful of snipers everywhere to keep just a pair of ships from knocking out your commands. I'd also recommend not heading out until your friend has 'auto-explore'd a few waves of basic scouts. If you feel a need to see more of the universe, the best thing to do is not scout yourself, but knock out all the tachyon guardians, making it much easier for your friend's scouts to travel the distance. There's less chance of triggering something nasty this way.
Try to develop a feel for what AI systems will draw a patrol; you can make a very effective distraction if your friend needs to strike elsewhere. On the other hand, you may need your human friend to take out a portion of the core shield generator network if you just cannot get anything done (if the patrol is 'at rest' on a chokepoint) In most cases, one collapses the entire 'letter' of csg, making operations much easier, but there are still other things the patrols will go out of their way to protect.
If you're not already using it, check out Ctrl-M; you can save a few layouts to quickly switch between. Most times not very necessary, but helpful if one of the AIs has a fondness for some particularly nasty bonus ship in their waves.
As a player with a champion ally, I like to set up a few engineers at a rally point where I don't have production going on, this way champions can head here for a quick repair/remodule without having to fight for the engineers attention. You should also be able to quickly respec your modules near a large nebula starbase.
Most guard posts won't raise AIP at all, and they're the number one source of reinforcements and hard limiter on the number of "Guardians" that can show up in a system. Command stations themselves are actually pretty fragile, just leave that to your friend to pop unless you're both trying to skip a few systems in order to reach much further into AI territory.