Question

I cant put multiple inputs it only registers two and ignores the third.

Answer 1

What DAW are you using? If you're using Studio One Prime you will only be able to record two tracks at a time.

Answer 2

I don't think Prime limits the number of input sources.

My guess is that you just need to configure your Song with the full extent of available inputs.

Ctrl + Period

Song Setup

Audio I/O Setup

Inputs

From here you can manually add the rest of your input sources.

If it is Presonus hardware I am surprised it didn't populate automatically.  Maybe verify that it shows that hardware on that dialog.