CSS is a method of appying a wide selection of styling attributes to existing markup. It enables you to standardise your site design and layout quickly and simply plus it also gives you a far greater control over the individual attributes associated with each element.
Finally as CSS allows you to remove styling from individual elements and create common styles (either on a page or across your site) this means that a page may actually end up being a smaller after you move to CSS which is good for your users since smaller pages = fast loading.
Obviously this will depend on how much you use font, colour and layout attributes at the moment.
SSI (Server-Side-Includes) is a method whereby you can build up what the client percieves as a "complete" page out of a variety of common files which get included into pages, also they may allow the use of a programming language to dynamically build a page.
This allows you to build aspects of your site dynamically before they are passed to the client - this means that you can create a wonderfully modular site structure with re-use of common elements while the client sees complete pages which gets you the best of both worlds.
Let me give you an example;
My site was CSS+ASP (think SSI with a programming language) based from the start, a few months ago I dropped it out of frames and had a little redesign (went from a dark green theme to a brighter blue theme).
I started by modifying the common stylesheet to use a new set of colours in place of the old, the real work here was not changing it but deciding if it looked good or not!
Similarly as all the common page elements were based around scripting with the headers and footers being built up by code (which allows them to have a common look & feel while having differing titles, descriptions etc) as so a number of elements needed to be added (or expanded) to make pages work better as pure standalone pages.
Thanks to using SSI & CSS some otherwise complex changes were accomplished in a few hours over a weekend. Changes to a few files replicated themselves across every page on the site - by editing a handful of key files I avoided the need to edit approximately 200 pages with a complex set of changes.
As technologies they both attempt to make it easier for you to maintain your website so using them together often makes sense since CSS is of the most use when your site features common aspects which need common styling.
If these aspects are indeed common then it makes sense to have one copy used everywhere rather than have a unique version on every page hence SSI may be a good idea.
Could you do what you want with a little markup + CSS? Yes, definetely! At its most basic CSS allows you to define background colours, text colours, heights, widths, margins, borders, padding etc.
If I read it right you are really just looking for a simple 3 component banner with no really complex markup which CSS could handle easily - you could use a DIV based design with internal left and right floating DIVs or just apply some styling to a 3 column table.
Whether or not you want to use SSI (or even server-side script) really just comes down to how you want to run your site.
I'm not really all that sure I can help with your navigation question though!