This looks like a really nice project, I'm backing it!
On the Stencyl side, can you tell us a bit more about how you used it? Tricks learned and limitations found along the way so far? How are you organizing such a big project for example?
As for how we used Stencyl, I suppose the way we use it for Hollow Knight isn't fundamentally different from the way you use it for smaller projects. It was originally going to be a much smaller project, but as we worked on it we saw potential and began to expand it. One thing we do a little differently is that we only have a single tile, a black square, that we use to build the terrain. All of the other bits of terrain (eg rocky ground, lamp posts, crumbling ruins) are actors set to minimal. This allows a lot more freedom when constructing scenes, resulting in a much more organic look.
One limitation of Stencyl is that it's hard to have more than one person working on it at a time. When one person is just doing art and one is coding it's not an issue, but if you both need access to the Stencyl file then things get awkward pretty quickly. For instance, trying to have one person build enemy actors and then have those actors into Stencyl often results in duplicated behaviours, because any behaviours on the actor being imported are copied over rather than just replaced with the same behaviour already existing in the destination file. On a project this size, it isn't too much hassle, but I can see it being a headache if you wanted multiple dedicated coders working at once.
Transferring scenes is also impossible through the Stencyl interface - we tried looking at some alternatives (eg. copying the scene files over manually and updating the scenes.xml ourselves) but these were all cumbersome and also had the potential to corrupt files. I've also had a fair few hiccups with the Windows compiler, but for some reason that seems to be a problem only my machine has. Maybe a Windows 8 thing?
Those limitations aside, working in Stencyl has been fantastic. Ideas come together really easily and the tools are all intuitive. We definitely couldn't have come so far in such a short amount of time without it. And like I said, there was no trick to getting this all working - the game is being built the same way as any other project, just more actors/scenes/behaviours etc.