I am trying to figure out which polyswitches to use for circuit protection. I am controlling a series of motors with an 8 channel relay. Each motor draws .8A at 12v. Only one motor should be on at one time. The power supply is a DC 12v 3A with which I want to power the arduino through the VIN pin and the motors through the relays. The poly switches have a large gap between the holding amps and the trip amps so I am not sure what I should aim for, if I should get polyswitches that are 1A holding and trip at 2.2A or something lower. Ideally it trips just above 1A but should handle .8 just fine, but that doesn't exist so it would be great if someone could provide some insight on this. I have found some info about polyswitches on here but not specifying these kinds of things.
Also, I've been reading a lot about the VIN pin for powering the arduino but I am still not 100% sure that goes to the regulator to convert the 12v to 5.5v.
Vin goes to the regulator. Vcc or 5V pin is the output of the regulator.
Motors tend to have a starting surge - make sure that this won't trip it (though, polyfuses have a non-instant response, so take that into account). Polyfuses are pretty cheap, I'd probably play around with a few values and see what worked.
Make sure you have diodes in place to clamp the back EMF from the motors, and the relays that you're controlling the motors with (most relay boards do all this correctly, but I've seen some horribad relay boards sold online..)
One thing that's missing in your description is how you plan to power the relays. The relay board will need minimum 1A at 5VDC (I would recommend 1.5A). If you has a 12V relay board, you could use the same supply as the motors (12V). For this board, you should have a separate 5V supply.
Here's a great way to connect it up and get full isolation. Yes, the relays on the board have the diodes installed, you can see them just below each relay. The 4-pin ICs just below that are the opto-couplers.
The polyswitch you mentioned (1A holding and trip at 2.2A ) is a good choice, I wouldn't go lower or higher.
Thanks for the clarification on the polyswitches. I have a 12v 3A power supply for it, which means I can only run 3 motors at once I guess. Can i use the 12v PS to give the board 5v?