Npackd always creates a new directory during the installation of a package version. Normally the name of this directory is the package title (e.g. "Firefox"). If this directory already exists the version number is used as a suffix (e.g. "Firefox-27.0.1"). If this directory is also already there an underscore and a number is used additionally (e.g. "Firefox-27.0.1_2", "Firefox-27.0.1_3", etc.)
There is no way to define where a package should be installed exactly. As you would probably define a dependency on the main software package in each plugin anyway, I'd recommend something like this:
<dependency package="com.mycompany.WordProcessor" versions="[5.00.2195, 6.1)">
<variable>WP</variable>
</dependency>
<file path=".Npackd\Install.bat">copy spellcheck.dll "%WP%\plugins"</file>