Hopefully I can explain this a little better in text to help you guys.
When fully transformed and in a morph you will roll a bit differently, obviously. When it comes to rolls using INT, WIS or CHA you roll with your main character sheet and as normal. You will add your own Proficiency.
UNLESS your current morph has Proficiency in the skill you are rolling. THEN you will add your morph’s Proficiency bonus to said skill roll. Yes, in addition to your own Proficiency bonus.
When rolls using physical stuff (STR, CON and DEX) come up, you are now reliant upon your morph. You will roll with their numbers instead. You don’t have a Modifier/Score to worry about though, it’s just the given number.
HOWEVER if you roll for a skill that you have points in with your base form, you DO get to add the skill points to the roll. You do NOT get to add any physical proficiency to rolls made in morph. For example if you have 6 points in Athletics as a human plus your Proficiency bonus, you will add the +6 but not your proficiency in addition to whatever your morph gains.
Certain things about your characters and their experiences will effect these rolls, but it works more on your DCs and not your rolls.