When connected to a running X20CP3686x, it says it's offline

[alexander.hefner]

Hi,

but actually the two are separated in general am I right?

Yes, you’re right. Internal and CF flash are two separated memories, there’s no interaction between them. You can choose which memory to use by the mode switch, but only exclusive usage is possible (you can’t use both at the same time).

how exactly do I upload software inside the PLC, and not with the CF card.

This should possible by preparing a USB Stick with the suitable project using AS (please see here, scenario 2c), plug the stick into the PLC and switch the PLC to BOOT mode by using the Boot/Reset button (please see here in the help, and some more information in the solution of this thread).

Another option could be switching the PLC to BOOT mode and do an installation online - please see this thread for a perfect description how to do it:

How to Reset a PLC without Removable Media

There are times when you want to completely factory reset a PLC back to the state it came in from B&R. This can be useful for testing deployment procedures or recovering in the worst-case scenario. The following procedure will walk you through removing and resetting the PLC to as close to from B&R factory state as possible. This procedure applies to any of the following targets (list is not exhaustive or updated regularly): X20CP04xx, X20EMxxx, X20CP13xx, X90CPxxx, 4PPC30, 4PPC70. 1. Place t…

Hope that helps a bit.
Best regards!