If you're wanting a 'self guided' tour why use a company to arrange it? Cycling in Czech, Slovakia and Austria is relatively simple. A good selection of campsites, guest houses, supermarkets (Lidl, Aldi, Penny Market). If I can be of further assitance I'd be glad to answer your questions, just message me.
Toby's hostel in Prague makes a good, well priced, free unlimited coffee (!!) starting point.