I was planning on running the frozen reaches for my players soon, but I wanted the mass combat to be bait more interesting. I know the rules from Battlefleet Koronus aren't well liked, so I was thinking about using the new rules from the Tome of Blood.

What is everyone's take on them, and are there any pitfalls I should look out for when converting the troops, etc.?

I have not bought it yet but I have heard good things about mass combat in Only War. You might try that if it's not a hardship to buy just for those rules. I am thinking of getting it for that very reason.