The threshold for medical is any amount exceeding 3% of your net income...and yes, enter all your expenses. The software will complete the calculation for you. In fact the full amount is also recorded on the tax return.
http://www.cra-arc.gc.ca/tx/ndvdls/tpcs/ncm-tx/rtrn/cmpltng/ddctns/lns300-350/330-331/menu-eng.html#...
