We had Kate's "sleep" area downstairs when we brought her home, Eric and I slept in the spare room on the same floor to tend to her throughout the night. We go to bed around 10pm, she usually would need to pee around 12:30am, 3am and then again around 5:30am (which is wake-up time for me anyhow)...
Then it just slowed-down completely. She would only get up once throughout the night, around 3am.
Now (at 5 mnths) Kate sleeps on her cot in our bedroom, and we have to wake her up in the morning (lazy girl)!
But - as soon as she's woken up - she goes straight outside for a pee...
I guess what I'm saying is I think a lot of it comes with maturity, but I do think moving Iz's crate out of your bedroom would be a good idea. He'll whine for a bit (but) he'll put himself to sleep. Also, are you keeping any lights on at night? We did for a while, but found Kate would whine a lot more with a light on. Now, if I'm getting ready for bed (and Kate wants to sleep), she'll whine at me until I turn the light off - then she's out!
When Kate went from being let out 3 times throughout the night to once - it literally happened overnight. I think she just hit a spurt where she "understood"...
Hope this helps - good luck (and) try to squeeze in a quick nap or two if you can in the evenings!