Let's face it. This will not be the last time
Custom Web Design redesign your website. At the time I write this, thefreecountry.com has gone through at least 5 different site designs since its creation. Tastes change, as do web dynamics. And as you get more experienced with your site, you may find that things that once seemed like a good idea hinder your site's growth. As a result, the redesign that may currently appear to you like the-design-to-end-all-designs will eventually be changed as well.
To reduce the amount of hassle that you have to go through every time you make a site design change, it's probably best to invest in a sophisticated web editor that is designed to manage such site changes. Most free web editors don't really have the advanced site management tools that a full-blown commercial web editor like Dreamweaver provides. Even though these free editors have "site" or "project" facilities, they are rudimentary at best. Commercial editors like Dreamweaver allow you to change your web design on a single "template" page and have all your changes automatically replicated across all the pages on your site that depend on that template. (See my tutorial on How to Use Templates to Manage Your Website in Dreamweaver CS3 for details if you are interested.) You will thus not need to waste a lot of time doing search and replace operations and manual fixing of the odd page by hand.
Although I have in the past eschewed WYSIWYG web editors to design web sites, preferring to code HTML and CSS by hand, the situation has become mostly unmanageable now that I have so many pages on my sites. Note that contrary to what you may think, you don't need to have thousands of pages for the situation to become unwieldy; a hundred or so pages is enough for it to become a nightmare. As a result, most of the newest pages on my newer sites like howtohaven.com are managed using Dreamweaver's template system. It's true that these commercial editors are expensive, but when your site grows beyond a few pages and you're faced with the need to modify its design, the cost will more than pay back for itself through the time you save.