Nope, how this works is as follows:
1. You use the guild extract to upload the initial roster into the MEMBERS table.
2. Your guild members are flagged in the SV.lua file as "YourGuild" - and when they use their Character Profiler Addon to upload their data, the script makes a check against the MEMBERS table. If it finds their name in there, it checks again to make sure the guild name matches the guild in their SV.lua file - if so, it adds the character information to various tables, the main one being PLAYERS (and stores the ID from the MEMBERS table as a link).
If the guild name does not match...it disregards and moves to the next. This was built this way so that guilds could snag only their members' "tagged" characters. For example I have Medar, Megar, and Radem - but only Medar is tagged as SSB. I don't really want the others uploading...
Now with a few minor changes to the wowdb.php file, YES you can have everything upload.