Normal pages are created via "wombat newpage", new blog posts via "wombat newpost". Check "wombat help" for other commands. If you create a page and a folder with the same name (without the suffix), all sub-pages in the folder are listed on that parent page before its content.
Image galleries were added as a sort of pre-stage - place your jpg files outside of the stage0 - stage2 folders in the corresponding gallery folder (default but not necessarily only folder: photos). wombat generates web-suitable and thumbnail versions of them and places them inside stage0.
stage0 is where you edit your ordinary pages or formerly created blog pages (default but not necessarily only folder: blog). stage1 is created for internal reasons only, stage2 contains the files you upload to a suitable server, possibly via rsync to keep traffic low.
To customize the look and feel or the top navigation, edit the files 'style.css' and 'template', the latter being a Go template that is executed on every html or markdown fragment to create a web page.