I'm unconventional, in that I hate syncing my iPhone to my Mac (I try to have as little to do with iTunes as I can). Because of this, I operate my iPhone separate from my Mac if at all possible, so I have no folders synced. I do download my photos to iPhoto, but what I do then is just put them into a folder with the date on it.
What I use is an App called "iPic Manager", there are many such folder-type apps available from the Apps Store. You can create different folders within this App, each is capable of storing 100 images. So, if you run out of space, simply create a new folder. Within the app, I click on "bring from device", this opens up my camera roll, and I simply click on the images I want to send to the folder in iPic Manager. I then have to manually delete the image from my camera roll afterwards, but at least I know they're stored in iPic Manager in neat folders. And if I click on "save to device" I can then bring them back to the camera roll. With iPic Manager, you can have your images in the App AS WELL AS on your camera roll, deleting them from one does not affect the other.