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So, it talks about how you can have 3 aspiring champions as an HQ choice.. Can they all have different marks from different gods? 

I wanted to have one be Nurgle, one Undivided and the last one unmarked.  How does it work since marks work differently in Lost and the Damned?

now that is a very interesting question. mind if I add something similar.
the Lost and the Damned List quotes that Marine units with another Mark than undivided count as elites. what if the HQ, Champions, Lt. or allied Chaos Lord, has the same Mark?

The rule for the LatD list that says a CSM unit with a Mark other than MoCU is counts as Elite is separate from the rules in the CSM codex.  The CSM codex allows the units with a Mark the same as their Leader to count as Troops.  The LatD rules don't have the special provision for Marks that are the same as the Leader, so I would have to say that they are always Elites.  The LatD army list has several aspects that are similar to the CSM army list, but it is a separate army list and it has separate rules.  For the units with Mark to count as Troops, the LatD would need to make that permission, which it does not.

It kinda stinks they short change the mark benefits a bit. Tacit, whats your take on the HQ Champions using different marks?

Eye of Terror, Page 43: (Paraphrase) Each Champion can take wargear at the points listed in the armory and the points listed for the Marks below.

It appears that each Champion has access to the armory separately.  The Champions will operate in different units, so I don't see the Marks conflicting.  I'd say go for it.  I'm trying to look into it more closely, but you are permitted to give a Mark of Chaos to each of the Champions, and there appears to be no restriction on taking Marks of a different kind.

Thats what I was thinking but I figured I would offer it up to Dakka for some scrutiny.  Now I can continue organizing my new army.