I will assume that you would like to keep your sequence file and all its vis and sub vis used together.
The best way to keep all your sequence files and vi's and sub vi's together is to use a workspace and source code control method. The source code control can make sure that you save all the required files and sequences in a given location and hence you have all the required files.
The next release of TestStand will allow you to have workspaces and provide integration with Source code control which are compatible to MS SCC standard.
Anand Jain Applications Engineer National Instruments http://www.ni.com/ask