Do I need to have two separate custom plans with different start plans if I am using park hopper ticket and touring USF and IOA the same day ? The custom plan making process seamed to make chose just one.
Yes, you need to create two.
As @PrincipalTinker said, you need to make two. Simply make the start time of your second park plan coincide with the end time of your first park plan (plus some time to get from the first park to the second). Then you can optimize your plan and you are good to go!