1) You need to just insert a break for the duration that you expect to be eating. For quick service in park, expect 45 minutes. If leaving the park, you'll need a lot longer.
2) Not sure I understand your second question. So, you made up two separate plans, one for Universal, one for Island of Adventure? TP doesn't merge plans because you could be making two separate plans for two different groups that will be going to different parks that day. You need to set your time parameters, e.g., US from 9 am until 2 pm, then, set time parameters on your IoA plan from 2:30-9 pm, for example, and have two separate plans for different parts of your day. If that doesn't answer your question, then reply and clarify.