As far as I have learnt, correct spelling only comes with practice. When you are reading something it might not be possible for you to actually write down every word you are uncomfortable with. My suggestions is this :
1. Read a lot. Keep reading without bothering to remember the spelling.In due course of time, your mind will adjust to finding out errors in spelling with ease.
2. Write a paragraph everyday. I have seen that writing a paragraph everyday helps me learn and memorize the spellings of new words. Once you have started writing a few words, you will find it hard not to remember the spellings :)