Is there a way to manually add macromedia flash movie file to website made
through photoshop (while I'm still in photoshop)? Or do I need to add the flash
html code afterward? Any help is greatly appreciated.

I'm just guessing how this would work based on the way you had to do these
things with Fireworks. You make a slice in your Photoshop/Imageready layout big
enough to contain your Flash movie. After Imageready does its thing, open the
HTML file, and replace the contents of that table cell with the code you got
when you published your Flash movie. Have to watch out because if it doesn't
fit just right then your slices won't fit up right