Currently making a 4-layer PCB. I used the Freerouting autoroute tool. I just don’t know how to be sure my Vias are connected to their correct layers.
simplest option is to see of their are any “air wires”, the indication that certain nodes are not connected. Also run the DRC to ensure all the design rules, including connectivity, are valid and are met
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how do I check for air wires?
Visually I’m afraid, these are what indicates what is connected to what according to you schematic. I think a DRC run is your first priority as I feel you have more problems than that although it’s hard to see without the board in front of me. That’s a much as I can offer as I am no fan of ‘autorouters’ (like a lot of us 
) in fact I am one of the worst as I refuse to accept they exist and It’s just a bad dream 
However the DRC will be very revealing.
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With normal vias (Yellow circle inside white ring) always go through the whole PCB, and they always connect to copper on all layers that touches the via.
There are other via types (blind and buried), but those vias look differently. These other via types also are unlikely to be useful for your fist PCB (They are non standard, and cost extra. Usually they are only used on high density designs.
You can inspect your via’s from all sides in the 3D viewer. If you disable viewing of the PCB itself and of the soldermask layers (which cover nearly anything) you can look through the PCB, inspect the vias in detail.
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My DRC only has two errors, and they are regarding clearance violation on a few signals
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