Personally I could always tell the difference between minor, dom 7th, aug, dim, 9th, min6, min7 etc as they all have their own unique 'flavour'. I never had to question that from day-one.
The best way to work out how chords work is to work out songs. Listen to a couple of Beatles songs and then work out the chords to them.
As far as ear training goes, what I did was to play famous tunes, such as Pink Panther, Odd Couple, Bewitched - in fact any silly catchy tune I could think of.
After a while I found that I could play any tune on the guitar that i could whistle. If I can whistle it - I can play it straight off.
That's how I approached it.
Lee