I found answer thanks to #org-mode group on freenode
I have problem with org-agenda-list and org-todo-list functions, they break my windows splits and split emacs to 2 equal windows, is there any way to fix it? Or any other function for load todo/agenda in current active window? I have workaround with winner-undo (but it pissing me off).
Emacs window layout before function calls

Emacs after functions call

Set org-agenda-window-setup in your init.el
Thanks to quicksilver from #org-mode on freenode
Type
C-h v org-agenda-window-setupfor other options.