I have found pants but there is no spot in the paper doll system to equip them.

Correct. The 'pantaloons' you have found are an Easter egg that you carry over to SoA and ToB.

Make sure Jaheira is carrying them. She will press them for you.

Put your left leg through the left side and your right leg through the right side. Pull the zipper up, do the button and you're set.

I have a better way to equip pants, but it only works if you are playing BG2, or a BG2 mod like TuTu or Trilogy. (It might work on the Enhanced Edition.) It works as follows:

1. Use the cheat CreateItem("killsw01"); this will spawn a Long Sword +2.
2. Equip your main character with that Long Sword +2. (Don't worry if your main character can't equip Long Swords; they will be able to equip this one anyway.)
3. While the sword is equipped, get a game over. (Note that the sword has to be active for this to work; if the weapon is swapped for another, or if a magically created weapon (including those created by polymorph effects) is active at the time of the game over, it won't count.

If you can do this, you will then unlock the ability to equip pants.

(On a more serious note, if you actually try this, you will find step 3 to be harder than you might expect (assuming you aren't familiar with the mentioned cheat).)

Edit: Added missing parenthesis.

Edit 2: Why was this post "low rated"?

If you find all 3 pairs they combine in to a special armor in Throne of Bhaal.

I can't get this exploit to work, can you elaborate?