I haven't done a big Fair Isle project but I have done odd bits. Sally's advice to start simple is good.
How I learnt was to keep the main colour in my right hand and knit that the usual British way, then to hold the contrast colour in my left hand and knit those stitches the Continental way. It sounds a bit complicated but it does work
That way you can keep the two balls of yarn well separated.
I think the trick is to dominate your yarn, not to let it be the boss
Once you get that organised then you will be knitting with more flow and your tension will be more even.