The top of the Motor can be quite intimidating. Just make your connections one at a time, and you'll be fine.
The 6mm hose with the Y splitter goes from the lower "dust" port on the Pneumatics Enclosure to the dedusting and air seal port on the motor.
The 6mm hose goes from upper "tool" port on the Pneumatics Enclosure to the Tool Change port.
After that the two kool connectors each get a water line, with female kool connector.
Finally the Power UVW port gets the Spindle cable from the VFD and NPN signal wire gets wired with a smaller 4 pin connector to the MTR port on the Pneumatic Enclosure.
It is unfortunate that the NPN Port wire, and the Spindle Cable Wire are so long, and we wish they were about 12" shorter to be easier to manage, but that wasn't something that could be accomplished.
Zip Ties can come in handy here, but other holding options are actively being investigated.
ATC Motor Mounting Position
When installing the ATC motor... it's recommend that you lower the Z all the way down to the bottom. Insert the motor so it sets upon the bed... tighten the mount then raise it.
Now you're ready to Program your ATC in Masso