After you've created or edited a position using animtools, remember to save the file with a TXT file extension. TXT files can be attached directly to forum posts and they're easier for everyone to use -- no need to bother with ZIP files.
basically how do you make her left leg go in front of the girl =P
I know what you mean, but these pronouns are ambiguous. Please try to be as descriptive as possible when you're talking about changes (or bugs) in posing and animation. For example: "how do you make the seated character's left leg appear in the foreground so that it partially occults the kneeling character?"
I don't know whether this feature exists in animtools.
@sby might be able to clarify the situation or suggest an alternative.
also how do i make her head be lower without it looking unnatural
I've edited the position file slightly so that the resting position of the girl's neck is further forward
(well ... technically I didn't move the head at all; I pulled the shoulders back so that the spine is less kinked). If that's not what you meant, then please try to describe it in greater detail -- or sketch a few arrows onto a screenshot.