It will only write the new rom the first time you set the rom with ppre. If you make a bunch of changes but do not write a new rom before closing ppre, or if you name the new rom the same thing as the old one, the only thing you can do to continue to edit that file is to delete your tpm folder. Of course, if you made changes without writing, they will be lost, so... just remember to "save" your work each time by writing a new file once all your work for that session is complete.
Basically, if you don't see the window come up for ndstool, then it's not writing. It should only take 1 or 2 minutes to finish. The ndstool window will close on it's own when the operation is complete.
Also, I have not tried writing the rom multiple times without closing ppre, but if you are doing this and if you suspect that causes it to not write properly on subsequent presses, then simply only "save" once, close ppre, and then do what you have to do to set the rom and work on it later. PPRE remember all the changes you made (that it is able to write), so you can go edit trainers, close that window, and then go edit pokemon, close that window, and hit "write," and all of them will be applied at once.