Why exactly do you want it to be JSP? Any particular reason?
Do you want the site to be dynamic with a 'Content Management System' or a 'Shopping cart'? Like JhonCena mentioned, PHP is much popular and widely accepted language.
Tryout these tutorials for JSP, on these websites:
I prefer 'notebook' for my coding. If you are looking for a good web builder, try out the trial of Adobe Dreamweaver 8. There are many free editors like Notepad++4.0.1. And Eclipse might be a good choice since you want an editor for jsp.
To Incorporate flash you would need to develop/design the flash components separately. I recommend you to tryout Adobe Flash 8. You can download the trial versions from Adobe. It is the best, but a costly software to develop flash elements. Anyone who can suggest freewares?