Many towns have very specific codes relating to these installations and most require a wood stove permit and on-site inspection by either the building inspector or fire chief.
I like http://www.woodheat.org and especially their article(s) on chimneys and how important it is to have them be warm and within the heated area of the house as opposed to cold and outside. You don't want to put a wood stove in your basement. See: http://www.woodheat.org/chimneys.htm and http://www.woodheat.org/evilchim.htm and http://www.nrcan.gc.ca/es/erb/reed/wood/07_e.html
The sad thing is, once you read these articles you will know a lot more than the vast majority of general contractors (this was true of myself until recently) and architects.
You need all the help you can get, and remember that "a little bit of knowledge can be a dangerous thing" and in this case it could burn your house down and void your homeowners insurance. (your insurance company might have requirements of its own)