Firstly the reptilians would need to become intelligent, this doesn't require anything fancy that we know about, interaction with their environment and normal flukes of evolution could have caused this over time. But to have humanoids as well you could have the following.
At least two continents separated for a long long time or always separate would be more interesting as they would have evolved totally differently from the first mud crawling fish.
If you want climate to be a factor in retarding humanoid evolution, make their continent like Australia, mostly desert with humanoids fully occupied with grubbing around for food, and scarce easy to get to natural resources and land not suitable for large scale agriculture without additional fertilisation.
Reptilian Overlords became dominant on one and were so superior in technology and perhaps brute force that when they invented sea travel and found the other continent in which the humanoids were evolving they just took over and used the local fauna for whatever it was best suited for in their terms.
Breeding the humanoids into the forms best suited for them would depend on what they needed. Most likely they would breed for docility, loyalty and obedience as we have with dogs.