Can anyone help me with what software to use to design a basic template for all of my home theater installs? And how to go about getting started?

Sean, I am not sure I understand your question. Are you looking for software to design the graphical elements (backgrounds, buttons etc) or the software to edit the set-up of your MX-3000? I use PaintShop Pro for the former and the standard MX-3000 Editor found on this site (is there any alternative) for the latter.

Also on this site in the file section are several templates desinged by the members here, you can look through these and get some ideas / help as well.

I am able to download some of the custom ccf files off this website. I used the one by Ian Duncan "Apple OS-MX". I need to change the Direct Tv button to be a Dish Networks button. I need the XM button to be a sirius button. Ian gives a blank button at the back of the configuration, however, I don't know where to get the overlay to put the dish network logo on the blank button and how to edit it in my software, Paint shop pro 9.

In the editor, click on the button you want to edit. To the right under IMAGE you should see a 'before' image (and maybe an 'after' image). There are two buttons just above the image called 'export' and 'import' ... click on 'export' and save the image where you can retrieve it using Paint Shop (it will remain a .bmp, .jpg, .gif, .png etc. so you can open it with any external graphic editor).

This site is a good resource for graphics...under the files section you should be able to find Dish Networks and Sirius graphics (or do a google search for the images you need)

When you are done with your changes, use the 'import' button to retrieve your newly edited graphic.