Windows Server 2008R2 File Share permissions

Hello All, I'm having a lot of issues with file permissions and sharing on a 2008R2 server. I have an E: partition that I've created several subfolders and I'm trying to allow users access through mapped drives, but the permissions don't appear to be applying correctly. I have the following subfolders:

Apps
Jobs
Shared

Under those folders, there are subfolders which should have permissions too. I have Domain Users set to be able to access the shared folder and modify it, but they are unable to write anything to the folder. They receive an access denied. The mapped drive does show them the folder, but they are unable to modify anything. However, if I right-click on the actual E: drive and select share and give everyone full control, they are able to modify the folders. The only problem is that now they have full control of the other folders, Jobs and Apps, that they shouldn't have access to. I've read some technet articles that say the only thing you should need to setup is the NTFS (security tab) permissions because that controls local and network access to folders. I've tried breaking the inheritance and manually setting the NTFS permissions on the folder to with no luck. The only thing that seems to allow them access is by sharing the E: drive, which gives them the full control. UAC is disabled on the server, but I don't think that would make a difference. Any help would be greatly appreciated!