You can leave it in place unless you are installing a very large HSF that requires you to tighten it from the side. A Cooler Master Hyper 212+ can be installed in place, a Thermalright Silver Arrow requires you to remove the motherboard anyway.
That's good to know, because a CM 212+ is exactly the kind of CPU cooler I'd like to install eventually. I just wanted to know I could just buy it later and install it w/o removing the mobo and making everything a mess.
Thanks a lot for the info.