I think that if you start building your site from the groundup in Dreamweaver, and publish as you go, your subdomains will be alright. Shouldn't cause any problems. I would take a whole chunk at a time, though. Like...do your entire primary domain, then publish and move to the next one. If you have som pages of a domain or sub-domain in FP and some pages in DW...you could potentially run into problems, depending on how you build. I really think you'll be alright though.
As for whether or not your site will look the same across browsers...that's a whole other beast. Unfortunately, no program can guarantee how your site will look. A lot of it is just simply up to you. DW writes better code than FP (imo), but it is not perfect. Test your pages in different browsers before you publish and most importantly, jump in and get your hands dirty with some html coding. I taught myself to be comfortable working with the code. HTML is not hard to figure out, especially using DW's code view!
Good luck! There are several of us to help you out with DW as you learn!!