Yeah, not sure about that first issue - it may not be possible to do with a batch file only, although it is very simple to do with scripting; either vbscript, or autohotkey/autoit.
When you say you've trieed changing the title, I assume you meant that you've used the command:
start "window1" ... and that it's your program that actually opens up another command prompt.
If that the case, then there isn't very much you can do (easily) - I believe it is possible to change window titles after they'vee been opened using some native windows API calls, but this would be a little messy and not easy.
The easiest solution I can see (if it's possible for what you want), is to change the name of ne of the executable programs, s that it opens the command prompt with it's own name.