I am a little confused on how I should have my ten...

Depends on how big your setup is. If its a smaller tent in the range of 5x5 and smaller. I would say no secondary intake fan is needed just one exhaust. I have multiple vents on the bottom of my tent for passive intake of air plus one main exhaust fan pulling air into the tent via the bottom vents and pushing it out the top though a carbon filter. There are multiple ways you can set your filter and fan up as well, some people do not use a filter at all. I choose to have everything inside my tent so it looks clean from the outside but others put the fan and filters on the outside. essentially two ways this works, 1) your exhaust fan is in the tent and is sucking old air and pushing it outside the tent/outdoors, Or 2) Your exhaust fan is outside the tent sucking air and pushing it outside the tent/outdoors. If you use a carbon filter for smells they can be attached on either end of the system. Eg at the intake of the exhaust fan on at the exit of the exhaust fan. I run my tent so it sucks the air though the filter inside the tent and the air coming out of the tent is free of smells and particles. It take up more head room in the tent but it looks nicer to me. https://m.media-amazon.com/images/S/aplus-media/vc/b67b70ae-8a2c-43bb-bea1-3cd4671681b8.__CR0,0,300,300_PT0_SX300_V1___.jpg This is a visual image from amazon to look at. good Luck!