Retrofitting DOWNTUBE Battery to VERTICAL DROP IN Battery Cage. Advice, tips?

So I acquired a gently used, step-through ebike with a behind the seat VERTICAL Battery Cage without battery. I have a DOWNTUBE Battery with mount of the proper voltage which I tested with alligator clips and it was good to go. The DOWNTUBE battery mount will just fit inside the VERTICAL Battery Cage so if I can figure out how to properly attach them I'll have a runner. Two questions if you don't mind:

1.) Removing the VERTICAL Battery cage and opening the controller compartment gives me plenty of access to remove the old Vertical Plug. I'm left with a gaping 1x1 sqaure hole to run the wires for the DOWNTUBE mount down to the controller but also has 4 threaded holds to affix some kind of cover. I'm sure I can stumble through the task of weatherproofing my 'square-hole-round-wires' dilemma but wanted to see if anyone had any tried and true, proven solution to this that might save me time. Any any other tips on retrofitting DOWNTUBE Batteries to VERTICAL Mount would be appreciated too....

2.) I opened up the controller compartment to check things out and noticed there were two small, open holes in the BOTTOM of the compartment open to the elements and this appears to be OEM configuration. My guess is heat dissipation Is this normal?