How can a person have a value system and boundaries that's based solely on conscience?
An system of ethics grounded in conscience is difficult but not impossible to construct. It is much harder to develop and follow than a system imposed from the outside, but many thinkers, both religious and secular, argue that external frameworks really aren't ethical.
For example, imagine you live in an Islamic country under sharia law. You follow all the dictates of sharia law, and all the teachings of your particular school of Islam because there are external penalties for disobeying and rewards for obeying (i.e. lucrative jobs might be more likely to go to those seen as observant than to those seen as infidels). Many Muslims would argue that simply acting like this out of fear of punishment and desire for political advantage is actually not pleasing to Allah, but that it is more important to be motivated by genuine piety.
Acting out of conscience means thinking through what things are right and wrong in detail for yourself and then acting accordingly, rather than just guiding your actions by avoiding things your society punishes. In fact, Chinese dissidents or the Protestant reformers go against the law because they believe that doing so is right. A famous dissident, one who rebelled against the Jewish and Roman laws of his period, and argued that you must consult your own conscience, said:
"The letter killeth but the spirit giveth life." (St. Paul,
2 Cor. 3:6).