I have to ask - why are you not deploying to a catalog? That would solve all of your questions and issues.
If you must deploy to the file system, then you need to change the deployment model in VS - switching from project deployment to package deployment. Then, you need to setup and utilize a configuration for the package - generally that is a configuration file but could also be done using a table source.
Once you have that tested and working - you can build the package(s). Deployment only requires the dtsx and configuration file - as far as I recall and can be done with a simple copy/paste to the desired server location.