Connecting tools that are far apart in a big workflow is challenging.
My suggestion:
When you right click on the tool you want to connect FROM one of the menu choices would be "Connect From" which you would select. If the tool has multiple outputs (like a join for example) there would be a sub-menu with list of outputs.)
Then you would navigate to the tool you want to connect to (I use the overview window all the time) and right click on the tool you want to connect TO and there would be a menu choice "Connect To". Again - if there are multiple inputs then there would be a sub-menu.
I'd expect Alteryx to remember the tool you connected from, so if you wanted to connect to multiple tools (say from an input file) you could just go to the next tool and right click and "Connect To" would be available.
Cheers,
Bob