If you set your email up as imap instead of pop3 then as you delete the messages off of your home computer they'll get wiped from your Droid at the same time. Hope this helps.
Ive seen two possible solutions to this problem.
2) Dump the stock POP3 email app that comes with the phone and get K9 Email App. It works 100X better and has 100's of personal settings and modifications over the original. Plus it has a "Select All" button.