Monotreatment is bad because?

Certain antibiotics target the different forms of the bacteria.

Also, the different classes of antibiotics work differently to attack the bacteria. So combining two from different classes will be more effective.

One combo might be using a cell wall agent plus a protein inhibitor (amoxy plus clarithromycin)
(Burrascano - Advanced Topics in lyme Disease)

..and it is also thought that it prevents resistance if you use more than one antibiotic.

Yes, you should be addressing the cyst form. Tinidazole and Flagyl are known cyst busters.
For non-Pharma - you could try Grapefruit Seed Extract.

Also it is suggested that pulsing the lyme antibiotics is another method to deal with the cyst form.