Travelling in Thailand is relatively simple. Here is my advise.
Train. When it is possible always choose the train as your way of transport.
Trains in Thailand are reliable, inexpensive and clean.
Although trains are not very fast buses are not much faster and certainly less safe.
Buses are a big gamble.
You can travel practically everywhere in Thailand by bus.
There are hundreds of bus companies some more dependable than others, but you will hear even of a lot of scams related with bus travelling.
You should also consider other forms of transport, particularly for short distances.