We currently run our SSIS packages as SQL server agent job with the package source as "file system"
what are the benefits or differences if we import the package into Integration services and change the package source to reflect the new location?
There are two places you can store your packages: on the file system or in the msdb database. Each storage option has its own pros and cons and which option you choose will be based on what is more important to you. It also depends on scenario under which you are developing your packages such as FileSystem for ease of use but MSDB better for security purpose
Functionality Best in MSDB -
Functionality Best in File System -
You can have look of below article for more details.