If you book it as a single flight number (CO 50/51) as IAH-EWR then you do not get to pick your seats, and if the IAH-EWR segment is late you will potentially miss your EWR-FRA flight.

Try booking it as a multi-segment flight on co.com and for the low cost of a few extra dollars in taxes you get to pick your seats in advance and a few extra miles, too, though the misconnect issue remains.

And if you want to book through an agent don't take that lip from them. Simply reply "because I do; please book the ticket now" if you're embarrassed about explaining it or explain it. They've all heard stranger stories.