If .ear or .war file was installed manually via WAS Admin's Console after all installation steps, user will be presented with screen to confirm successful installation. There are few active buttons at the bottom something like "Save", "Cancel" and "Manage Applications". If user clicks "Manage Applications" he will be redirected to page where app can be started/paused/deleted and app files will be stored under
C:\IBM\WAS\Profiles\customWas85\wstemp\0\workspace\cells\USERNAMENode01Cell\applications\app.ear\app.ear
If user selects "Save" in above mentioned page, installed app files will be transferred to
C:\IBM\WAS\Profiles\customWas85\installedApps\USERNAMENode01Cell\app.ear
I would assume first approach uses some temp workspace folder "wstemp", second approach uses directory defined in "WebSphere Variables" as APP_INSTALL_ROOT.
This is confirmation for my observations
Uploading your application
The install process begins by first uploading your application file (EAR) to a temp directory. If you are using the administrative console to install your application, wstemp is used as the temporary working directory. For example:
profile_root/wstemp/0/upload/app_name.ear
Processing installation options
After your application file has been uploaded, the installation options are read in, processed, and written to your installedApps directory:
profile_root/installedApps
Saving deployment metadata
At this point, the install process stores the EAR file in the following directory:
profile_root/config/cells/cell_name/applications/app_name.ear/