A lot of the Tibet based agencies can also arrange tours of Tibet for those starting in Nepal. Companies like Tibet Highland Tours and Snow Lion Tours (as well as many others) should be able to easily arrange all of the tour details for you if you begin in Nepal.
Do be aware that there are more restrictions on foreign travelers who go from Nepal to Tibet and then on to Mainland China. You can only enter on a Group Chinese Visa, which the travel agency must arrange for you. This Group Chinese Visa is normally only valid for 21 to 28 days and cannot be extended. If you plan to take a 10 or 12 day tour of Tibet, you might not have enough time remaining on your visa to explore the other areas of China you are planning to go to. To avoid this restriction, do your trip in the reverse order (if your travel plans allow you to). By beginning in Mainland China and then going to Tibet and Nepal, you avoid the limited duration Group Chinese Visa restriction and can enter on a 30 or 60 day normal Chinese Tourist Visa, which can be extended in any major city in China (except Lhasa) for an additional 30 days.