We've had Sophie since she was 8 weeks and she’s now 15 weeks.  She’s a lucky girl because my husband works from home and so they keep each other company through the day.  But the problem is that we think we have a major dependency issue on our hands.  While she loves her crate, sleeps through the night in there, and happily runs in and out of it during the day with toys, she does not do well if we put her in her crate when she doesn't want to be in it. Whether we put her in and stay in the room, or leave the room but stay in the house, or leave the house all together, she screams non-stop.  It’s hard to believe something that small can make sounds like that! We’ve done the positive association with the crate thing, we’ve tried to only let her out when she’s not screaming (hard when she barely stops to take a breath!), we’ve kept her in a crate only big enough for her to lay down, and we’ve tried waiting it out… and nothing has worked. In fact, when we left her for a short while, she peed all over her bed. If she’s tired enough she will sometimes fall asleep within a few minutes but otherwise she just gets more and more worked up.  We exercise her like crazy – she’s getting at least 2-3 hours a day at the off leash dog park. I don’t think that’s the answer.  Does anyone have any advice or step by step instructions on how to deal with this?  We love being with her but right now we can’t leave her alone ever without her having a melt down and peeing in her crate. 

Consider for a moment that the crate isn't the actual issue here.  The issue may be your dog's feelings towards who's in charge.  

I believe some of this behavior stems from your doggie's belief that she is somewhat of the pack leader still.   Just keep enforcing that you make the decisions and she must obey, and soon she will realize that she only needs to follow and not be in charge.

The mentality of pack animals allows the alpha to wander wherever it pleases, and the pack stays or follows. The pack is not allowed to leave without the alpha though. When your pooch feels it is the alpha in the family (or in some part alpha-ish) it will see you leaving and have issues being stuck in the crate because it can no longer keep tabs on you. This is what causes separation anxiety.

Mine had sep. anxiety the fist 2 days she was home with me after I adopted her. Once I began leading her on walks, and teaching sit-stay-come and ENFORCING the boundaries and limitations I set for her, she became relaxed in me leaving the house or room, knowing that she no longer had the responsibility of caring for me because I was in charge. She is much happier as well.

Good luck! Be firm and consistent and she will love you for it! Trust me!