I have moved to INDI/EKOS recently and would like to use my usb/bluetooth modul rather than another cable like eqdir, how do I do this? Is it supported?

It shouldn't be different than a regular USB cable I believe. Just set your port to the USB-Bluetooth port (usually /dev/rfcomm0) under Options. This assumes you have configured the USB bluetooth adapter already and it's online and connected.

So EQDir <---> USB/Bluetooth <---> Bluetooth on PC running Ekos

I am using just that configuration with my HEQ5.
Just make sure you first pair your bluetooth adapters (with bluetooth manager for example) and then issue a bind on them with this command before connecting:

sudo rfcomm bind hci0 xx:xx:xx:xx:xx:xx, where the xx, correspond to the mac address digits of your mount bluetooth adapter.

It works fine!

Well, responded too soon!!!!
Just updated and.... I does not work, EQMod Driver starts but I can't connect to port rfcomm0
It simple does nothing when I press the Connect button.

Downgraded to
ibindi1_1.3.1+r2749~201611301615~ubuntu16.04.1_amd64.deb and
indi-eqmod_0.3+r2747~201611290934~ubuntu16.04.1_amd64.deb and it works again,
There is some problem with the updated lib/driver.

I have solved the problem it works now. I had trouble with the raspi 3 bluetooth configuration. I have followed the guidelines given by www.datenreise.de/raspberry-pi-3-bluetooth-verbinden/
Usually the dev/rfcomm0 can be defined by editing the /etc/bluetooth/rfcomm.conf but this did not work on my raspi 3, don't know why. To fix it I have create a script that is run at startup of the raspi to define and bind to rfcomm0 by issueing the following command: sudo rfcomm0 bind hci0 mac-address 1

Thanks for your help

Great! Glad you solved the problem.
Also EQMod is working fine now after today's update.