Hi,
Have you read the documentation starting here:
http://www.mojoportal.com/creatingskins.aspx
Most work in designing a skin is in css. layout.master is for adding things that you want to be on every page like links or images or google ad scripts. css is used for all layout and style.
There is a different layout.master file in each mojo skin so first you have to make sure you are modifying the one that it is using based on the selected skin in site settings.
If you have further questions after reading the docs, please be specific. Which layout.master file did you modify(i.e. where is it located)? What modification did you make? What did you expect to happen?
Hope it helps,
Joe