Hi Shubhada,
It sounds like you're using the package import feature properly as outlined in:
https://casecomplete.zendesk.com/entries/21933278-sharing-items-between-projects
When using this method, your imported package(s) will always be put into the package of your choice in the destination project, and cannot "replace" the top level. Similarly, only sub-packages from your template project (i.e., not the top level itself) can be imported.
For your goals, it sounds like a "Save As" might be the right course. Once you've created and saved your template project just right, you can actually create a new project directly from that template, rather than importing it into another existing project.
Click File / Save As on the ribbon bar.
Choose option 1, Keep existing filename. You can modify the existing file names if you like, but it's not necessary (see attached).
Save your project with a new name, in a new folder after clicking Continue Save As.
This will create a duplicate of your template project in the new location, which you can continue to modify as necessary.
Let us know if you'd like any additional help.
Jason