Hi @Slav, i remember back in the day the autotrader bot would do the courier missions also which came with the trader bot. That doesn't seem to work anymore? Unless my settings are wrong so i bought the courier bot too, i tick the option but still doesn't do it. Please help. Thank you

First of all you need to switch to courier bot on the same client and tune it as per manual. Check that everything works. Then you switch to autotrader on the same client and enable interface.

So do I have to do a first run with the courier as well as the auto trader?

Do first run when courier is selected. Don't forget to remove drones as courier needs overview expanded at whole height.
Autotrader may use any first run as it does not leave station in default config.

This didn't work, so I did the first run with courier, then I ran the courier bot and it worked fine. When I check the box on auto tltrader to run courier as well as soon as I go back to the front page the check box unchecked and then doesn't work at all. I am quite confused.

You mix two modes: remote trader + collector and courier interface.
Collector's task is to transport all cargo around Perimeter/Jita to Jita. Courier task is to transport mission cargo to another station (not Jita). That is why both modes will not work if activated at the same time.

Also you need different first run for remote trader + collector. If collector is selected as algorithm, first run will add player citadels to stations preset. Courier does not need citadels visible in overview.