controlling window-configuration changes

[knubee]

 i realize that questions about window configurations are faqs, but i
have not been able to find an answer to this particular question.

i tend to split my emacs frame so that there are two buffers side by
side (C-x 3). this works fine, but there are some applications that
insist on using the entire emacs frame when they are invoked (org-mode
agenda view, TOC for latex files, etc.)

is there a way to specify that all apps respect the vertical boundary
of the current window? or does this require configuring something for
each of the offending apps?

related question: when using moinmoin mode with screen-lines.el, long
lines are wrapped appropriately if the window is the size of the full
emacs frame. But dividing the frame into two side-by-side windows does
not work. Then, the lines of text have the right-facing arrows (to
indicate that the lines continue beyond the right-hand edge). Is there
a way to fix this (or some other utility for long lines) that will
respect the edge of the window?

thanks.