I also take Armour and I did find that splitting the dose worked better for me. You can try it and see how it works for you. I know someone who takes it once in the am and she feels fine taking it that way. It depends on each individual. The best way is the way that works best for you.
You can go the Armour site to find the conversion chart to ensure it is the correct dosage.
As far as side effects I haven't had any. I felt soooooo much better on it almost immediately. I hope you will as well!