I have recently Installed TES4Gecko, and have two problems/questions. The first is, will I have troubles If I change a file that must be a master to a plugin to edit, then back into a esm?
This is safe as long as no other plugins depend on records in the master that will be affected by your changes, so make iterative saves with each major change or playtest after each major change to be sure your plugins survive your revisions.
And also, why can't TES4Gecko "Find my Oblivion"?
Try the "Set Directory" button.