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Siege weapons are rather restricted in its use, but that doesn’t mean one shouldn’t think about using them.  If you just toss them in, you might find that they don’t make sense or fail to get a decent impact.  There isn’t anything necessarily wrong about just mentioning them being there, but readers tend to expect such things to serve a purpose.  So, what are some things to consider when using siege weapons?

1. As I said, it isn’t a bad thing to mention them while describing a large scale battle.  It can become an issue if you are writing scenes during the ensuing battle and they aren’t operating.  These things are something that allies need to get around, protect, and be careful of.  If they are close enough to attack the wall then you will have trouble describing the fortifications as being unscathed.  So, you need to think about how they will affect a scene if you identify their presence.
2. Research how siege weapons work.  This is very useful if you want your heroes to find a way to destroy them.  It also means that you can have characters talk about the mechanisms and make repairs without making stuff up.  People seem to be able to pick up on when a mechanical device is being incorrectly described.  Another benefit of research is figuring out ways to make unique versions for your world.
3. Even though siege weapons are typically only found in large battles, you don’t have to always restrict them to these scenes.  There can be a small group who have one of these devices and are going to use it for something other than war.  For example, a bandit group might have stolen a mobile ram to use on a treasury or a sealed cave.  Heroes might even need to get one for special circumstances.
4. Getting launched by a catapult can be funny, but people can’t realistically survive it.  Still, you can tweak reality with magic or just hoping readers don’t care.
5. Siege weapons do not operate themselves.  Remember that even modern day versions have teams making sure they are loaded, aimed, and fired correctly.  So, a hero trying to defeat a siege weapon can’t run up to it and bash away since there will be enemies to fight through.  Even non-warriors assigned to use them will pose an obstacle.  Again, you might have to research how many people are needed to effectively use them.
6. Some siege weapons can be used in traps.  This requires some creativity, but I’ve seen it done in various D&D games.  For example, we had one game where thieves set up a ballista on the opposite of a door.  Open it up without disarming the switch and you get hit by a giant bolt from point blank range.
7. In large battles, having a siege weapon malfunction or get destroyed can create a massive mess.  Consider what will happen to the people around these things if they are defeated.  A siege tower can fall on people, a catapult can misfire into friends, or anything shooting fiery objects has the possibility of an explosion.