I hate tangled workflows too!
The connections to any tool are highlighted when that tool is selected, as you probably know. That is often useful to visually see where the connected tools are.
Sometimes when you insert a tool (like a Select) in the earlier stages of a workflow, this then tabulates the downstream tools to default distances. This can help, but sometimes it then makes connections to parallel flows look messy. So use in appropriate circumstances.
Once you get a group of tools nicely spaced, you can click and drag your mouse to highlight the whole group, then move them around together.
In terms of hiding groups of tools, you could add them into a Container, then minimise the container when you don't want to see them. Then drag single or groups of tools out of the container as you're ready to place them as you want them.
One final tip might be to turn certain connections to wireless. Don't over use these, because then it is hard to see at a glance where the connection goes to, but this method certainly has its place when trying to tidy up a messy workflow.
I hope these tips help.
