What is the best way to prove or disprove a potential new gene? It has already been proven to be dominant and gives a certain phenotype, BUT there already exists a dominant gene that produces the same/very similar (depending on who you talk to) phenotype.

 

This 'new' thing needs to be either proved or disproved as being on a different locus, and if it is on the same locus needs to be proved or disproved to be a new allele.

 

Please excuse the terminology, I'm new to anything more in depth than predicting genotype/phenotype outcomes so I hope it makes sense!

Genes cannot be proven/disproven. Either a locus is getting transcribed, or it is not. If you want to find a linkage between, say, an allele and a phenotype (something further down the role), the experimental path would depend on the system/organism under investigation and the phenotype in question. E.g. phenotypes on the cellular level are more accessible to certain types of experiments as, say more complex and less well defined ones on the population level.