Bit late but nobody really answered the core question yet so:

Intake fans: Intake fans are generally used in conjunction with exhaust fans to create airflow and improve cooling. This is why computers have two fans (at least) and so forth.

Exhaust fans: In addition to the above, exhaust fans are also used to control emissions/pollutants. If your printer has an exhaust fan it should, bare minimum, have a cheap carbon filter attached to it. A proper exhaust system is theoretically better but that tends to be better handled as a fume hood.

So when would you use either? A rule of thumb is that exhaust should probably always be on (while printing) if only to mitigate fumes and particulates. Even with the door open it will still help a bit. This applies to both "safe" filaments like PLA and outright toxic stuff like ABS.

As for intake? You probably also want it on any time the exhaust fan is on (so always) just to improve airflow and make the exhaust fan more effective. You aren't going to pull a vacuum without it but it still helps.

So when would you control them separately? I would probably say "never" but I could see a case where you have a particularly toxic low temperature/fragile filament (like TPU cut with a lot of ABS or something?) combined with a fragile print. You want as much filtering as possible for health reasons but you want to minimize air flow to minimize premature cooling or even the risk of "blowing down the print" as it were.

So... yeah. I would very much lean towards just having the intake/exhaust on the same controller.