除了+肯定词、句 means in addition，常用：除了...还/也/都 除了+否定词、句means except

除了= except in anywhere/anytime(like subtraction in maths).他受伤后,除了大拇指可以活动,其它指头都不能动了.After hurts his thumb can moving but others finger can't moving. 除了我生病没来以外,其它同学都参加了这个聚会.Excep me, others classmate were joined this party. 这次考试除了数学没及格,英语和物理都及格了. Excep maths,English and physical both were passed in the exam./ English and physical both were passed in this exam without maths. in addition= 另外 or 还有(complement,like plus in maths ) 请把这件衣服洗干净,另外那双鞋子也需要清洗了.pls wash this close,also(or in addition) wash that shoes.

It depends on the logic of the whole sentence. There is a method of helping you to get the meaning of "除了" faster, though: If there is a corresponding term "还" in the same sentence, "除了" usually means "in addition". However, as there may be some exceptions, you cannot count on that. After all, it's not difficult to grasp the logic of the whole sentence.

unlike western language where the words make the meaning of the sentence -- in Chinese the sentence indicates the meaning of the word so as you read the whole sentence you finally get whether it's "in addition to" or "except"

You don't. You have to guess according to the context. It's same as "apart from" which can be either "in addition to" or "except".