The bar is likely to bruise you no matter where you have it, if it's your first time (or first time in a while) - that's not a sign it's in the wrong place. But if you do choose to do high bar make sure it's sitting on your trap muscles and not actually pushed against your neck.
I think when many people attempt low bar, they have the bar TOO low - in a position where if you stood completely upright the bar would roll down your back if your hands weren't there. I aim for the shoulder blade area to find my sweet spot, however it didn't feel like it was "locking in" till I got used to it. With low bar you really need to squeeze your elbows up to form a "shelf" so the bar sits on the muscles.
There is the chance you could have it in the right place and it could be a flexilbility issue, where shoulder dislocations, wrist and pec stretches would come in.
You gotta just keep practicing and experimenting till you get it right unfortunately. Don't worry about your wrists being bent, as long as you can stand up straight and your back's taking the weight that's all that matters. Try wrapping your thumb round the bar if you're not already if it's still uncomfortable on the wrists.
There's links to related stretches at the bottom of that page.