First, welcome to the community. There are a number of Preferences you can make (JMP>Preferences). but I'm not sure exactly what you want. Styles lets you change tick marks, Graphs lets you change line width, etc. I'm sure someone with more knowledge will come by and post advice. For the percentage, as long as the column in the data table is setup as percentage, JMP will use that on the graphs.
"All models are wrong, some are useful" G.E.P. Box