I didn't find them on 1851 census and I looked under first and last names but here they are on 1861 census.
I looked up 1851 census on Ancestry.ca and also on
www.automatedgenealogy.com and did not find them.
1861 census Brant Canada West
MART
Wm, upholsterer, b England, Primitive Methodist, 42
Mrs, b England, Baptist, 49
Emily, 17, Upper Canada
Alice, 12, UC
Wm, 10, UC
On your family tree it says he and wife Amanda were married 1861. I finally figured out that children were from a first marriage.
Also tree indicates that William was born in Kingston 18 May 1851 but I didn't find them on any 1851 census there either but a lot of it is missing.
Some of the 1851 census has either been lost or destroyed. On the transcription that you saw, did it give an original page number?
Was their an obituary for either William? It may name Alice and Emily.