My two year old has 3 blister looking things, assuming they're canker sores. what can i do anything to help or will they just have to run their course?

Only to relieve pain: There is really nothing you could about them except for pain relief ii could use Lidocaine viscous or gel and apply it as needed on the canker sore.

Blister looking : There are numerous things that can cause "blister looking things" in the mouth including, but not limited to, canker sores, mucoceles, bacterial gum infections, abscessed tooth/teeth, etc. At 2 your son should have am ongoing relationship with a General Dentist or specialist Pedodontist for at least a year. Best for him to be seen and properly diagnosed.