How do Stigmatas and compatibility rate determine how powerful a Pandora is?
Just like Eumel said in his comment, you should just keep reading. This answer will contain several spoilers and most likely will spoil a lot of the plot. So you have been warned 

(scroll down to the TL:DNS; if you want a practical answer without spoilers)

To properly understand how stigma's work, you will first have to understand what the stigma's are. 


   Stigma's are pieces of Nova's, either obtain directly from a Nova 's core, or from the original Nova Maria Lancelot. They are known for their urging signals of destroying everything. 


The so called 'Compatibility' determines how much of the 'power' stored within the stigma can be used by the Pandora. Theoretically speaking this means that somebody with 10 stigma's with a bad compatibility could be weaker then somebody with 1 or 2 stigma's with a strong compatibility. 

However in the world of freezing stigmas are not limited to just one type:


   Besides regular stigma there are also the heroic stigma, A stigmatic body, the Type-Maria Stigmata, injection stigmata: plasma form, legendary Stigmata, Plasma Stigmata, Legendary Stigmata System


Each and every one of these have their own pro's cons. And even though compatibility still plays a huge role, the type of stigma also does. 

TL;DNS:

Yes it possible for someone with 1 stigmata to be stronger than someone with 5. This can be due to a person having a different type of stigmata, or significant better compatibility with the stigmata.