After installing the HKS hipermax RS at the shop, I noticed the upper rubber seats for the rear springs (the ones that look like a thick rubber funnel) isn't put in. Do I need to put it in?

Yes, they aren't supposed to be removed unless you are installing certain coilover setups, all spring setups reuse that rear rubber springmount

I installed coilovers btw

It depends on if you're using true coilovers, i dont know if the HKS is a true coilover. My Tein Basics have a seperate strut and spring in the rear so you have to reuse the stock rubber seats. If you have true coilovers then the rear will be a spring on the strut just like the front, therefore you wont have any need for the oem rubber seats in the bucket on the toe arm.
-GP-