My main issue to suggest this is that there is no documented standard on how eCS/Warp organizes the "Programs" folder. There is a un-documented standard for that folder that is "just drop things there without any order". The "Programs" folder is a mess, and some might like it or not.
Of course there is no documented standard. The programs folder is user modifiable, to make it the way the user wants it. The default is to sort by name, with folders first. Adjust the display to change it (including using the location where the user happens to drop something). However, that is not the best way to do it.
I use three main methods. One, I put my main icons on the desktop. That includes the Programs, and Internet, folders. They are the master access to everything. I would put Internet into the Programs folder, but I use it enough to justify having it on the desktop.
The second tier are a few often used programs that I just drop into eCenter (XCenter). No, I do not use the Tray widget, there is a better way.
The better way? I create a folder (I put it into the Utilities folder, but it can be anywhere), and put things into it that I want to use a lot (mostly shadows of programs). Then, i drop that folder into an eCenter (I have two of them). One click to open the folder (it expands), and one click to open whatever it is that I want to use (it can be a program, a file, or another folder in the first folder, which creates a sub menu).
Actually, there is a fourth method that I use. I use the Programs folder (sorted alphabetically, folders first), for things that i almost never use. That includes programs like QPDFView, which can be opened by simply clicking on a PDF file. There is rarely any need to open the program itself.
There are other ways, including using the Trays widget.
I try to follow two main rules (but they are only to guide myself). 1) Don't put anything on the desktop that doesn't make sense. 2) Keep it as simple as possible.
WarpIn was mentioned. If the installer is built properly, it will be able to find where the user put whatever it is, and update in place (even if the user moves it). Since the programmer has no idea where a user might want to put it, they should initially just put their work on the desktop, and let the user put it wherever they want it. Little effort is required to move something like the PMView folder off the desktop, and into an appropriate folder that the user chooses. The files, of course, need to go where they make sense. There are two default locations: Applications (bootdrive:\Programs by default, in eCS), and Tools (bootdrive:\Tools by default, in eCS). Neither one of them should be on a boot drive, it works a lot better if they are on a data/programs drive, and they can be shared between boot systems.
I could probably go on all night, but that should give you some ideas.