Q: iMac set up or desktop set up

I currently have a Macbook pro that I do most of my work on. I just received a promotion at work and will be working from home a lot more. I was going to buy the iMac 27 inch with retina 5k display as well as the Apple thunderbolt display. I have been attempting to do as much research as possible but have not found a good answer as of yet. My job with provide me with a laptop (which isn't Apple). When I work from home I want the ability to connect the laptop to my iMac and the thunderbolt monitor to have a dual monitors or just work off of my iMac with duel display. Would someone be able to break down the best way to do this and how. Also I noticed that the Apple thunderbolt display is not the same height as the iMac display so how would you fix this.

Sorry for the newbie question and thanks and advance.

-Wayne