I wanted to know if there is a way to create two separate option categories.

for example you get two proficiency's of your choice and one of three effects.

but i want to make it so that it doesn't show proficiencies with the second category and vise versa. 

I believe you would need 2 different subclass features. One for the pick a skill proficiency and one for pick an option.

I know, but I want to know if there is some way to do it. 

Yes there is.

1. Make a subclass feature.
   1. Add a modifier for proficiency / choose a skill
   2. Add a 2nd modifier for proficiency / choose a skill
2. Make a different subclass feature
   1. Check that this feature has options
   2. Fill out the levels that those options are available
   3. Add each option

If you have the PHB, copy the Battlemaster. The Student of War Feature lets the player choose a tool proficiency. Just change that to choose a skill and then add it a 2nd time. The Maneuvers feature, each maneuver is an option. Its a lot of options so it might be overwhelming but the Battlemaster subclass is the first one I looked up to see if it had something similar.