Re: How native English speaking people think, when they write?
Depending on how fast you type and the way you write, you may well mistype words that are homonyms of what you mean to write.
All the time, I'll find I've written "hear" instead of "here" and "your" instead of "you're." This is certainly not because I don't know the difference, but because the inner voice that is narrating what I'm writing simply says the word and my fingers make it come out.
Sometimes my eye will catch the error. Sometimes it's my my editor who does.
I think the fact that you're thinking in English as you go is actually a huge step. Getting the spelling right is just the final step!
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.