Alt click on a node connection automatically disconnect it from the other nodes. And there is some nodes which can be easily summoned by pressing a key and clicking at the same time. Like B+click will place a branch, and S+click a sequence.
If you're willing to compile it, Aseprite is a great option as well.
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Have a look at a simple and interesting description of the level design tests, created by game designer Robert Yang.
This is a test game companies send to level designers. They are given a piece of paper and are asked to draft a little structure of the level. Robert provided a number of ways this task could be done and gave comments on the shortcomings of these designs.
Also, if you are interested in the way level design work in popular 3d games, have a look at this amazing article we’ve done with Emilia Schatz and CGMA. She’d been building levels for Uncharted 4 and she’s a very talented designer, who knows this process to the smallest detail. You can also subscribe to her class for next year! She is also working on a book on level design, which you should be on the lookout for.