Check the fare and the name of the village and return services before you set out and try not to get into too many arguments about the price. The time to show a bit more concern about price is in chartering or hiring a vehicle. Hiring for use outside of the major towns might be difficult without some knowledge or help with the Indonesian language. To hire a vehicle you presently need your normal license plus an International endorsement but there is talk of a Bali-like 'temporary license' in the near future. Make sure you carry some sort of insurance as very few local companies will supply it.
Usual requirements are a substantial deposit and payment in advance.
From the moment you arrive in Timor you will have people approaching you and offering various services - tour guide is perhaps one of the happier alternatives. What it all costs will depend on your schedule and their workload but all the large hotels in Kupang and Dili either run or have affiliations with reputable tour companies, as does Merpati and Garuda Airline offices and some overseas travel agents. Then there are specialist companies and freelance operators working in or from the bars and smaller hotels all over Timor but, outside the major agencies, you will most likely end up paying for your guide's food, cigarettes, beer, etc. Make sure this goes into the initial calculations.