Did you know that through the Tactical Console (under the Gamemaster menu), you can run combats, including tracking initiative, status effects, spells, hp, etc. Everything except the actual dice rolling (which you can do using the Dice Roller).
You can also set up encounter portfolios with all the creatures in a certain encounter, then when the players come across that encounter, you can import the portfolio in with your Players portfolio, open the tactical console and hit go, and bam, everything is all set up for combat in seconds.
If you already knew these things, then great, but I kinda insinuated from the way your question was worded (and the fact that you're REALLY new to the forums) that you might not have known that Hero Lab is more than just a character creation software. It handles the rules just as much as Realm Works handles the story.