On most buses, the best seat is number 48. It is on the last row where the passage between seats ends. It lets you stretch both your legs and stand up – which are important on those 12 or 14 hour trips over gravel roads. Since seats are generally assigned, you will have to ask for it. ¿Puedo tengo asiento número cuarenta y ocho? (May I have seat number 48?) Should do the trick.
Of course, this can backfire sometimes. It is normal for buses in Bolivia to pick up passengers who will stand or sit in the isle and you’ll have to spend the entire/rest of the trip playing footsy with someone who gets crankier every time the bus hits one of the way-too-many bumps. All in all though I found the request generally worth the effort.