I had some visa issues and only have a 3 month single entry now. So Jim said extend work permit 2 months before expiry and come back to get a 1-year ME.
As there are no more direct flights from Samui, it's pretty shit. I went with the night train to Padang Besar last time and then onwards to Butterworth.
Works well for the way there but the way back has inconvenient times so I flew Penang-KL-Surat Thani to get back the same day. Cheaper than flights to Phuket and Samui.
There are some visa run agencies with very comfortable mini vans with wifi and power sockets on Samui it seems but I'm not a fan of buses in general so no experience with that. Only Songserm and that's THE HORROR!