I am a little confused about the use of these two words and how I have been taught to write them.

Ben saat sekizde çalişmaya gidiyorum. I am going to work at eight o´clock.

Sonra işe gidiyorum. After I am going to work.

Do both words mean the same or is there a reason why they are used in different sentences
?

Here are my thoughts

iş = work, job (noun)

çalışmak = to work, to try (verb), çalışmaya = verbal noun, (to) working

Ben saat sekizde çalişmaya gidiyorum. I am going working at eight o´clock. (At 8 o´clock I am going to do some sort of work) 

Sonra işe gidiyorum (gideceğim). Later I am going to (my) job. (Afterwards I will go to my workplace)

In English to work can mean either a place or an action, and the words are the same, whereas in Turkish the difference is less ambiguous because the action can be differentiated from the function/place.  

Çalışmak  in the first sentence is used to mean work out or physical training.

thank you both for your help