Dennis Sweeney's book
A Lancashire Triangle - Part Two has a section on the industrial railways of the Manchester Collieries.
Although Sweeney's focus is on the history of the area's LNWR lines rather than the L&Y, p.351 of the book has a map clearly showing the relationship of the Atherton line to the Manchester Collieries' (later to become NCB's) extensive private railway system in the vicinity of Little Hulton and Walkden.
Colliery railways crossed the Atherton line in three places:-
1. Just west of Mort Lane at Little Hulton - the colliery line between the end of the ex-LNWR mineral branch from Little Hulton Junc. (on the Bolton - Roe Green line) and the Peel Hall and New Lester pits.
2. Just west of Walkden High Level station, alongside Newearth Road - the line between Mosley Common colliery and the Manchester Collieries / NCB central workshops & loco shed at Walkden.
3. East of Walkden High Level - the colliery line between Sandhole colliery and Linnyshaw Moss.
At locations 1 & 2, the colliery lines passed beneath the Atherton line. At no. 3 the mineral line passed above, close to where the M60 now passes over the Atherton line.
This 1961 One Inch OS map (available at the National Library of Scotland website) clearly shows nos. 2 and 3.
Peel Hall and New Lester collieries had closed by the time this map was surveyed in the late 1950s and the remaining rail connection towards Little Hulton was from the Atherton line itself. However the underbridge for the former line to the coal mines can still be seen and its course is marked as a track.
Further west, several other colliery branches joined the Atherton line e.g. from Eatock pits, near Dobbs Brow Junc. and from the Hewlett pits at Hart Common, joining near Crow Nest Junc. However none of these actually crossed above or below the main line.
Further west still, approaching Wigan and not technically on the Atherton line as such, the L&Y main line passed above the - ahem - Springs Branch.