Navyeoseabee,
1. Click the MESSAGE icon > press Blackberry Button > Options > Main Message List Settings > uncheck your synced email account. Now you will only see the messages delivered in your Email icon.
Now the emails will not appear in your MESSAGE icon. You can also disable SMS and MMS here and they will only appear in the SMS icon. You could also turn off your data channel when you want complete silence but you will also lose other data services.
You could probably set up a filter in the BIS Server but I wouldn't even begin to be able to tell you how to do that. I fixed a duplicate message issue with Gmail by setting up a filter in the BIS Server, but I had a step by step instruction list that helped me set it up.
2. There is no "trick". To be absolutely sure your application is closed, simply press the Blackberry button and press "close" or chose the "log off" in the messenger programs.
3. Highlight the icon you wish to move, press the Blackberry button, select "move" and place the icon where you want it.
4. Always delete any programs you don't use. This will be a BUNCH. You can either do this by pressing: Options > Applications
This will take a few seconds but it will populate all the applications in a list for you. Then you can manually delete them one by one. This is the slower way and will require a reboot.
You can also use your DM, which I think is quicker. Then you can save an image of your phone with the new configuration. YES - your phone will run faster, nothing dramatic but you will notice it.
5. IMO - Probably the best case made for your Storm is the Otterbox. There are several but the newest one has a heavy duty belt clip - Otterbox Defender case. Check it out via the link below.
OtterBox Defender Case for BlackBerry Storm 9530 - ShopCrackBerry
Hope this helps!