I'm much more of a newbie at the DNA stuff than some of the other folks here, so I might be approaching the Custom Clusters with lower expectations.
I had already solved my two big DNA mysteries. Using this tool has been a way of visually confirming my findings, rather than helping me to solve them.
But I'm also trying to help a friend with some of her DNA mysteries and had been attempting to use the Leeds Method in an Excel spreadsheet for some of her DNA matches. The Custom Clusters showed me that two separate colour groups actually belonged with a third (her biggest and strongest group of matches). (This might have been obvious if most matches had had trees, or big enough trees.)
Anyway, being able to fold those colour groups into one has shown me the two other distinct groups I should focus on. So it's been helpful in that regard.
For visualizing my own DNA matches, I start with the widest range of cMs: 20-1300, then do 50-1300. For me, seeing the results has been a confirmation that I'm on the right track with my DNA sleuthing. I'm only using the one primary, targeted match in any given cluster. I started by adding others but it wasn't helpful for my purposes.