You can do this numerous ways, can use DNN  Forms authentication which is nothing more then forms authentication against a table in the DNN DB schema. OR use Active directory, etc tons of ways to do this.

As far as the file upload you can create user groups in DNN and set users to the groups, ALL possible via sql scripts managed by your exsisting application. (to save you the hassle of recreating the groups manually. You can then go in and set rights to the each folder in the file manager thusly allowing X group edit rights while Y group can just read.

If you able to code a complex authentication system, then altering the DNN forms authentication control should be a piece of cake. Its pretty simple method. Key thing to remeber, that minus the code, images and files you specify to save to the file system, everything DNN related is stored in the database. This gives you tons of options for managing DNN from an outside application. Also can look at the web.config file cause there is a user time out setting you might want to look into. The default is 2 hour timeout I think, it gets annoying for users, but is easily changed to what ever time frame you want.