Well after doing some searching I never did find out an exact way to do it as in step by step for someone who wouldn't know all the pc jargon or where to find certain things on a pc... Now that was the only hassle i ran into, not being able to find a guide or a in depth explanation. But once you figure it out, it's only a few very small steps and not a hassle at all.
When I said 50+ email address... i have a big +. I have about 3 sets of 50 accounts with 1 main account per set. The main account per set is above the matching set. So not only do I scroll to find the main account for each set, but also when I need to alter an auto reply or anything else on one of the accounts in the set, i'm scrolling through alllll of the accounts searching for that 1 account. now THIS is a huge hassle. so as you can see it would be tons easier for me to have it organized with separate instances. Especially since on top of that I have personal accounts too. When I added my personal accounts and "moved up" on each one to bring them above all the other accounts, each time thebat froze and filters in some of my accounts magically disappeared. Now, you can imagine how frustrating it was going through a little over 150 accounts checking each of the filters (there are about 5 on each account). ALWAYS make backups of your thebat before messing with tons of accounts.
Anyway, so I'm writing a step by step guide to help people who can't understand the other posts about this.....
How to Create Multiple Instances on The Bat...
1. Create short cut for every instant. Go to start > program files > thebat and right click on thebat.exe and choose "move to > desktop". Do this for every instant you'd like to make. For this guide let's say we are going to make 3.
2. Rename each short cut you find on your desktop. Let's rename them as follows...
1stbat
2ndbat
3rdbat
3. Next go to start > run
and type in
HKEY_CURRENT_USER\Software\RIT\The Bat!INSTANTNAME
so for us we will be doing...
HKEY_CURRENT_USER\Software\RIT\The Bat!1stbat then
HKEY_CURRENT_USER\Software\RIT\The Bat!2ndbat then
HKEY_CURRENT_USER\Software\RIT\The Bat!3rdbat
4. this is going to open up a new window or "instance" of thebat. go ahead and walk through the set up for each instance.
5. Go back to your desktop where the shortcuts are. right click on the shortcut and where it says
"C:\Program Files\The Bat!\thebat.exe"
in the target space... youll need to replace it with
"C:\Program Files\The Bat!\thebat.exe" /Reg:INSTANCENAME
so for us we will be doing....
"C:\Program Files\The Bat!\thebat.exe" /Reg:1stbat then
"C:\Program Files\The Bat!\thebat.exe" /Reg:2ndbat then
"C:\Program Files\The Bat!\thebat.exe" /Reg:3rdbat
and thats it

i hope this helps the not so savvy pc user

=^..^=