What were the steps you actually did to make it work?
What are the ownership/permissions of the files now that they are placed?
A great number of MineOS users have bukkit servers with any variety of plugins, including worldedit, without any loss of functionality in the web-ui. In creating your server, did you create a new profile? What were it’s settings?
It won’t be necessary to add to the GUI an editable field for teh start command, as plugins are loaded by their presence in the /plugins directory, not by whether they are listed in the start command.
Let me know what you did, and I’ll try to point out any accommodations that MineOS requires to make it work. For the most part, I see no reason why MineOS and the web-ui AS-IS couldn’t service your need as described.