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I Don't have my book yet, hopefully will get it the day it comes out, but from what I can understand you can mix charcters and units of different gods. Right now im planing on running a lvl 4 sorc of nurgle, a lvl 2 sorc of tzeentch, 2 units of Warriors with one to nurgle and one to tzeentch.(one of these units could become chosen, will have to see.) I'm wondering what the thoughs on puting the Nurgle Sorc with the unit of Tzeentch warriors. Mainly will the unit be giving -1BS to shooting because the Nurgle sorc is with them? This seem like a slight strech of the rules having one charcter affect an entire unit with something that is only working for him, but in a way it seems to me it's the same as having a lord of Khorn with frenzy causing his unit to charge just because he has the frenzy.
To you original question, Yes you may mix and match marks how you like.
To you other question, Characters that join a unit with 5+ rank and file cannot be targetted by shooting, so they cannot pass on the -1 to the unit, though he will be protected by their mark from shooting attacks as long as their still 5+
Given that shooting hits the unit, rather than being randomised among the models, I guess that is the case. So, how about in combat - does that still apply? Will models choosing to attack the character suffer a -1WS in combat? I'm assuming not, but would be happy to be told otherwise.
Check the wording on the MoN to respond to your question about CC. All units in base to base with a MoN model have their WS reduced, so they should always be affected by that. Note that the -1 WS isn't just to hit either, when you go to attack them, it also applies.
As for the Khorne hero making the whole unit charge... he doesnt. If the unit declares a charge, they do so as normal, but if the unit is not charging, and the Khornate is in range, he will charge out of the unit to go get some blood for the blood god.
The MoN will affect shooting for the whole unit as long as they are MoN and the character is not targetable (5+ rank and files). Note that this goes the reverse for a MoN character... since he cannot be targeted, it will not benefit the unit.