My 2 yr male doxie is very shy and fearful and has recently gotten much worse.?

We rescued him from Louisiana - a breeder got rid of him because he was too shy for their purposes. He is very lovable and at first was thriving with our family and becoming less fearful every day. We also have a 2 year old female who is very active - she is definitely the leader and sometimes plays too aggressively for his taste. Until recently they played happily together although he started having a few peeing accidents a few months ago if someone reached to pet him too quickly, etc. Now he pees every time we say his name, try to pet him, or even move anywhere near him. He spends most of his time cowering under furniture. If he rolls over for us to rub his belly, he pees as soon as we come near him. We can't let him in rooms with carpeting (which is nearly the entire house) and I can't imagine this behavior continuing. There is no abuse in my home although I suspect he was abused before we rescued him due to his shyness and cowering nature. But within the last few weeks he has become worse than when we rescued him 9 months ago! Any suggestions?