If you already have a bunch of monsters and Monster Groups set up, and just want to fight them - right-click on the map name on the left of your screen, and go to Map Properties. Double-click in the Enemy Encounters box and add in the Monster Groups that you want to be able to fight, one at a time. Set the encounter rate as well - the lower the number, the more often you get attacked.
If you're absolutely new, and don't know how to make monsters yet.. BLUECUBE MONSTER TUTORIAL GO!
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Step 1 - you need to have a monster to fight. RM2k3 has a bunch by default, but we'll make our own for now. Go into the Database and pick the Monster tab. Click on the Array Size button and change the value from 115 to 116. This alllows us to add another monster (we always could delete the old ones, but for now let's stick with adding a new one.) We'll make this one a ghost monster. Give it a name of some sort.
Click on the Set button, to the right of the black square. Scroll to the monster called "Ghost". Use the color alteration scrollbar if you want to mess around with the color, and hit OK. Now, we want the ghost to be transparent and fly, so go ahead and check those boxes. "Flying" means it'll hover up and down during battle, and "Transparent" is rather obvous - it'll make the monster see-through.
We'll give him these stats: 100 HP, 50 Attack, 30 Intellect, 12 MP, 30 Defense, and 30 Agility. Make him worth 50 EXP and 100 GP, and change the Item to Potion, with a 100% probability of dropping it.
Now, we'll give him some sort of skill, so it just doesn't attack turn after turn (that's boring.) In the behavior section, double-click under Attack. When the Monster Behavior box comes up, click the Skill radio button and choose "Fire 1" from the combo box. (It's in the second half of the list). Hit OK. Now, it'll randomly cast Fire 1 (which costs 4 MP by default, allowing him 3 casts per battle).
It should look like this:
Click the Apply button to save your changes. Now click the M. Groups tab, right next to the Monster tab. We'll increase this section's Array Size as well - set it to 89. Now click on the new blank line (89) and pick your ghost monster out of the list on the right. Click "Add" twice to add it to the group twice. You'll see your monsters appear in the mock battle screen - you can move them around if you want. Click on the Autoname Group button to.. automatically name your group. If you want, you can rename this.
From here, you can follow the instructions at the very top of this post to add it to a random encounter. If you have any trouble with this, let me know..