My friend Sue Swiggum of TheShipsList wrote out this explanation which she gave permission to publish on Olive Tree Genealogy Blog
The different types of border records require a different approach, so researchers will be learning as they go. These will also be a great asset for finding US destined passengers on the recently uploaded "Canadian Passenger Lists, 1865-1922" which are unindexed.
Using the CANADA-US border records (St. Albans Lists) researchers will find ship name and date of Canadian sea-port arrival, so they'll have the records kept by two
countries, however, remember the border records only begin with 1895.
M1461 and M1463 are the Soundexed cards, card manifests,most commonly used. And from about 1927 to 1954 those cards are the actual border record. In those years, if the immigrant was coming directly across the border from a steamship arrival, the card relates to a ship list. The actual ship lists are on M1464 (Atlantic ports). So for the years ca. 1927 to 1954 there are two cards for those transiting Canada--a ship list and a border card manifest. For those coming from Canada in those years there is just the card manifest.
But for the earlier years, 1895 to 1927, the Soundex card manifest from M1461 is an abstract of information taken from a Border port list. The cards were made in the early 1940's by INS to make reference easier (searching by name rather than by year, month, port). The original border port record was a land border port list. These are inter-filed with the ship lists on M1464.
The point is that for the earlier years, 1895 to 1927, there can be three records for a transmigrant.
1. The Soundex manifest card.
2. The border port list from which the card was later made.
3. The ship list showing their arrival at the Canadian port.
If the immigrant is coming from Canada then there are just 2 records--the port list and the corresponding card.
I won't delve in to some of the confusing aspects which some people might encounter, but will attempt to answer queries to the TheShipsList@rootsweb.com mailing list on a case by case basis.