In Pathfinder, the Magus has several archetypes they may choose from. Based on the rules of archetypes, you may have several archetypes as long as they both don't modify the same class feature.
"A character can take more than one archetype and garner additional alternate class features, but none of the alternate class features can replace or alter the same class feature from the base class as another alternate class feature."
In PCGen there is a problem. If you are an elf AND magus, you can apply the 2 archetypes, Kensai and Spell Dancer. The problem lies in that both archetypes modify or replace the medium and heavy armor class features. You should only be able to apply one or the other.
Another problem exists with Bladebound and Spell Dancer. Both modify the Arcane Pool class feature.
When you apply the Spell Dancer archetype, PCGen does not give you the option to apply Bladebound. HOWEVER, if you apply Bladebound FIRST, you can then freely apply Spell Dancer with no problems, as long as you are an elf and a magus.