I've been wrestling with this for a while now and I need some advice or assistance. I have a subtheme with some created regions and I can't seem to get the default site-menu to display drop downs and trying to put the region in the place of the site-menu area seems to break different sections of the theme. Any advice is helpful.

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I personally use superfish for my dropdowns and have never had an issue with it breaking the layouts or sections. Just disable the main menu in your subtheme settings and then place the superfish block and you're off!

Sorry just saw this was in D6, I haven't played w/ dropdowns in D6 only D7 and superfish.

Thanks for the feedback, I would really like to use my D6 subtheme since I added all my regions and got really familiar with it. I'll maybe have my D7 ready soon if I can get some feedback on using drush and git to upgrade. Is anyone using the D6 Omega still ?

D6 is stable and not the recommended release so not too many people are building on it anymore unless they are heavily tied into D6 and can't upgrade. Most of the support you'll find here is related to D7 though.

Adding regions etc. in D7 isn't difficult at all so you should be able to update your theme structure without any major issues.