I download an addo-ons, and the install is just unzipping into the "Applications" subdirectory of the Mathematica base directory. However, I try to copy my application into the "Applications" without any add-ons in the "Document center". why?
I think you will have to state your question more clearly. What was the application that you were installing? Did you unzip it directly into the \
$UserBaseDirectory/Applications folder or \$BaseDirectory/Applications folder? You may have it at the wrong level or have created an extra level of folders. Unzipping will generally create a folder with the application name so you don't want to create an extra one. The file structure should look like: