Where do you put the MAC(i'm assuming you mean the MAC of the respective WLAN cards) of each partner in the WDS?
Yes, the MAC of the distant end WLAN card is entered into the wds "sub-device" of the near end WLAN card. You create this wds sub-device using the "wireless" window. Click the "+" sign and select wds as the item you want to add. As master device, select the WLAN card that you are using for this link. In the "mac address" section of this newly added wds device, enter the mac address of the wlan card at the opposite end of the link. Do this for both ends of the link.
Also, when you mean "pick one mac already assigned to a port" wouldn't that duplicate a MAC?, i mean, i have MAC for Ether1, MAC for WLAN1 and the random generated MAC for bridge1 on each endpoint
Consider that if you don't manually assign a mac to the bridge, it will pick a mac from one of its ports and assign that to itself. Yes, in a sense this duplicates the mac address, but not in a harmful way. The mac address of the bridge is just a way for the bridge to identify itself to the other bridges. As far as I can tell, this value isn't used for anything else. The drawback of letting the bridge pick an address for itself is that if one of its ports stops running, or if you swap out a radio card or disable a port for some reason, and that happens to be the device whose mac address the bridge had picked, it will pick a new mac address from among its other ports and mac forwarding temporarily stops until things get sorted out again. Picking a random mac address for the bridge won't hurt anything, but you need to insure you don't accidently pick the same random mac for any other bridge in your network. That duplication would be bad.