Disabling pcie slots is irrelevant. You can use both but it gets a bit more complicated in which the software will use. If you have multiple monitors, you can plug at least 1 into each and just change the main monitor in windows. If you only have 1 then you have to switch ports but this would only be a concern for which gpu is used for viewports or games. Some renderers will let you choose gpu and many gpu renderers will use both.