1) The guiding section of Ekos doesn't show up. Is the GP not recognised as a guiding camera (using indigo_ccd_iidc driver)? Do I need another driver?

INIDGO, unlike INDI, creates different devices for different purposes. You will probably find "Atik GP" device for camera itself and "Atik GP (guider)" for its guiding port, you can use them independently. You need to select first one as camera and second one as guider in Ekos. The same apply for "Atik One" and "Atik One (wheel)", there are two independent logical device too for a single physical unit.

2) The Align section (I used the INDIGO Telescope Simulator for now) won't work. I would like to use the EqMod telescope driver with a synscan mount but there doesn't seem to be (a stable) one in INDIGO. Can you run INDI EqMod and INDIGO CCD drivers side by side? If so, how?

SynScan driver (and also alignment model) made a huge progress during last couple of weeks, but binary package is not created yet. You can either checkout INDIGO from GitHub and compile from source ( github.com/indigo-astronomy/indigo ) or you can run INDI EqMod driver (or any other INDI driver), just prefix it with -i switch on a command line. This instruct indigo_server to load executable instead of dynamic library and to use legacy INDI protocol. I can't recommend this approach for e.g. CCD drivers as far as legacy INDI protocol is really a disaster from performance point of view, but it doesn't matter too much for mount driver.