I have not done this for a long time, but i will try to answer this using my limited knowledge.
For theme related changes, you will have to identify the FTL / SOY files which you need to change. You could use Browser's Inspect Element / FireBug tools to identify code elements that are involved in rendering the page. Doing a Keyword Search on these terms, in a fully compiled/ built Jive Project,
( Ref How To: Create a Custom Jive Project ) will list all the files where the element you need to change exists. ( mainly ftl, soy and *.js files) .
Once you know how the functionality is rendered by combination of these, you can figure out where all you need to tweak to achieve your customization.
For FTL & SOY files, you can make the changes in theme files directly ( assuming you are on 6 .0.x Version) and check by applying the theme.
Hope this helps.