This appears to be the major drawback with cms systems, and why I still use straight html, php, etc in my own sites.
This is what I've been doing for other people when I make a site for them with a cms and hopefully it will work for you:
a) I make one straight html template page with a menu for each section, not every page, of the site
b) In each page I enter all the necessary tags
c) Plus one sentence or paragraph (usually the first paragraph of the original page including <h> tags) and a second paragraph that says 'the page you are trying to locate can be found here' with a link to the cms page.
d) in each page is a 2 second refresh that sends the viewer to the correct cms page.
d) I also go into the control panel's redirect area and enter in a redirect for each html page to go to it's correct cms counterpart.
Hope this makes sense. What happens if someone stumbles upon the html page is
the redirect sends them to the correct page or failing that for some odd reason the 2 second refresh automatically sends them to the correct page.
The robots find the html page and sees the first paragraph and hopefully follows thru the top level menu on the html template page recording the information which hopefully gets into the search engine. And any visitors that arrive as a result of it will be redirected in one of two ways.
I've only recently implemented this since I noticed that the sites I made with a cms are not getting spidered as the straight html or php sites, so whether it is effective or not, time will tell. But it may be worth a try.
Alias all your pages. From what I understand most search enginees have limited supported for complex url structures like the default encoded ones used by phpwCMS.
