I was playing tonight and had a battle with 3 rows of different classes, ie: triangle, circle, and hexagon. Both of the first rows were done, meaning they had battled against his first 2 rows, and that left only the third row of hex's that had not attacked yet. My opponent had the hexagon "siege tower" 2 of them and all i had left were the triangle and circle units that had already attacked. Since his had not attacked yet, did that mean he draws fate cards and attacks my circle and triangle units that attacked earlier? Thats how we played it anyway. Please let me know.

Yes, you do each number in turn, but the damage applied can be to ANY of your units, not just the stuff in the same number.

It's possible (in fact, likely in many battles) that one or both players will have units for one initiative that the other player has none for. In that case, as you say, only that player draws cards for that round.

That is what I thought. Thanks for the feed back, it is good game.

Then i read the rules again and it made it very clear.