If I understand you correctly, you want a flat ceiling throughout the building with room-in-attic storage only over a small portion.
As NUTTSGT said, this shouldn't be any problem so long as the two types of trusses are an exact match. I'm assuming that the bottom cord of a room-in-attic truss will be larger than a normal truss since it has to be designed to carry more weight. This won't affect the ceiling height. It is possible that the top cords of the room-in-attic truss might also be larger than a normal truss. You should check with the manufacturer before you order to ensure that it won't affect the roof height.
Before you finalize your plans you need to consider what truss spacing you will use, the size of the attic access opening that you want, and the orientation of the attic access opening. For a pole barn without a ceiling or storage, 8' on center truss spacing is fine. If you want to add a ceiling, 2' or 4' spacing will make the job much easier. "Stock" attic trusses are generally designed for 2' on center spacing. However, 2' on center spacing limits you to a 22 1/2" wide attic access opening---which makes storing bulky objects awkward. If you were building a permanent stairway for attic trusses, you would normally create a wider opening and put heavier (or double) trusses on either side of the opening. You may want to do the same thing even if you are using a ladder for access just to allow for a bigger opening and/or changes at some future date.
For the little added cost involved, I would consider using attic trusses for the entire building (or at least for more than an 8' portion.
An attic truss is going to require a steep roof to gain height for a 7'+ ceiling. The added height will require more roofing materials as well as more expensive trusses. Depending on your needs, you might be satisfied with using storage trusses rather than attic trusses. (The only real difference is that storage trusses don't have to be as steep and will have less headroom.)
