Which would give more exp when running national quest, Mission exp. Percentage or Mission fixed exp?

This would depend on the values involved. You will have to work it out for yourself based on what cards you have and the missions you have available. If you are able to always select the longer missions that give the most EXP then the percentage cards may end up giving more. Some of the fixed value cards give a large bonus though. And it will depend on the level of buildings how much EXP you can earn.

Have a look at the EXP value for each mission and work out the value of the percentage bonuses you have available.