The standard version of BaseElements comes as fmp12 files, and there is a runtime application option as well. You need to copy the 3 BaseElements .fmp12 files, or the BaseElements runtime folder to a location on your hard drive.
BaseElements will let you import as many different solutions into a single copy as you prefer. However some developers like to keep multiple copies of BaseElements, one for each project or client, and this is perfectly fine within the licence agreement. In this way you can keep a single archive of each project's development.
You can also use FileMaker server, although you can only have one copy on each FileMaker Server at any one time.