Is the only way to do this to turn off the stop mask for a specific pad and then draw a new rectangle of the appropriate size and set it to the tStop layer?
If you're asking to make the stop mask larger, then you would select the polygon tool, select the tStop layer, then draw the polygon so it overlaps the existing stop mask; the two will combine to create a larger area as you would expect. If you're trying to make a stop mask smaller then you would need to modify the IC package and remove the pad completely, then manually create the stop mask and pad using the polygon tool.
When your project is complete it's always a good idea to doublecheck the results using a Gerber viewer (like GerbV, etc.).
Chagrin:
If you're asking to make the stop mask larger, then you would select the polygon tool, select the tStop layer, then draw the polygon so it overlaps the existing stop mask; the two will combine to create a larger area as you would expect. If you're trying to make a stop mask smaller then you would need to modify the IC package and remove the pad completely, then manually create the stop mask and pad using the polygon tool.When your project is complete it's always a good idea to doublecheck the results using a Gerber viewer (like GerbV, etc.).
My goal is to make the stop mask smaller. I read somewhere that the router will only work if you use the pre-made pads in eagle. Is this incorrect? I do have something worked out but I am not sure if it is the appropriate way to solve the problem. The first picture below is the original part with .5mm pitch SMD's. As you can see, the stop mask almost touches. The second picture is one where I turned off the stop mask on the pad and then placed a new polygon on top of it with the correct dimensions and assigned it to the tStop layer. Will this work?
big_tStop by jg1996business, on Flickr
small_tStop by jg1996business, on Flickr