The only substantial difference you will see at altitude is lower hop utilization, due to the lower boiling temperature. There is a place to enter your altitude in the equipment profile that will correct the utilization %. Boiloff rate is pretty much a product of surface area and boil vigor. Humidity, and to a lesser extent, other climate related things play smaller parts.
If you haven't already, you need to set up an equipment profile that vary closely matches your equipment and various volume losses during the brewing process. Here's a link to a video that explains how to do that:
http://brulosophy.com/2014/08/04/beersmith-tutorial-equipment-profile-setup/
If you use the BIAB process, this links to the video you want:
http://brulosophy.com/2014/08/11/beersmith-tutorial-biab-mash-profile-setup/
The great thing about BeerSmith software is that it allows you to make various adjustments to tailor it to fit your equipment and process. In order for the software to give you accurate information, it requires accurate inputs from the user. There's an entire library devoted to information on how to use the software. Here's a link to it:
http://beersmith.com/blog/beersmith-home-brewing-guide/
If you don't find anything there to address a question you have, there are some people here that know BeerSmith well and will be more than happy to help.