I think it would be cool if when you saved your project the saved files would be added into a sub folder, because whenever i save my project not only is the blend file there, but alot of other type of files too. And i dont think its possible to create a new folder while saving your project for the first time. So each time i want to save a armory project i have to make a folder manually, and it can get really annoying.
There should be no issues running multiple blends from same directory but I agree all of the temp files should be moved to sub directory. Will try to take care of that.
In the meantime you may also find this button useful when saving the project.