You are fortunate if you have separate jacks for each. If you have a gaming headset with just one plug for both you will need an adapter to split them apart. They are easy to find.
To directly answer your question: The difference is how the software works with them.
In Windows, if you right-click on the speaker icon you will find that there are both "Recording Devices" and "Playback devices" there. When you go into one or the other you are presented with whatever the computer thinks is connected so you can set a default, set levels, etc.
There are alternatives that can be considered, also. For less than $10 you can get a universal USB sound adapter. They work on PCs and Android Tablets with no extra software. They give you two jacks. The green one is always for speakers or headphones. I always keep a few of them around for situations where I want to know for sure how things are going to act. Most computers are smart enough to switch over to them when they are inserted then back to defaults when they are removed. And with that adapter I mentioned above they work fine with gaming headsets that have one plug for both. They're available from the usual sources.