Website into sub domain and Main Domain

Sorry to disappoint, but I think it's a bad idea, especially if your site already has some rankings. There is a good chance you will lose them if you do it like this.

Google treats subdomains, not as parts of your main site, but as completely separate sites. So your current site will not help rank your subdomain, and your links from your subdomain will not help your main site either because the subdomain is new and will transfer no link power.

My advice would be to continue with your current site. Flash is a problem only because it replaces text, so your content does not count as text content. Can you add text content below the flash / below the fold? That would take care of the problem.

But all that said, you are approaching SEO from the wrong end as it were. Relatively speaking, on-site SEO matters very little compared to your backlinks. On the Web, you are what your backlinks say you are, it's as simple as that. SEO Link Building (this info is my work) is the way to go about achieving your ranking goals. Optimize your site, for sure, but don't sweat it too much. Most importantly, make sure you have the right unique title tags on all the pages, with the right keyword placed at the very beginning of the title tag. Most importantly, optimize your site for conversions.

In terms of link development, as you will see from the thread that I referenced, the greatest challenge is gaining access to the right links. But if you have a sound business model and actually expect to make money from targeted traffic, then undoubtedly engaging a professional who will provide you with powerful backlinks and propel you exponentially in the search results is the obvious way to go. Links are the only indefinitely scalable aspect of SEO, everything else matters little by comparison. Don't waste money and time on redevelopment, just get the right links.

I hope this helps a bit!