1) As a noun this referred to the floor of a coal-pit, the underground part of the mining operation.
The word is recorded in the OED from 1778 and is said there to have been usually in the plural. In Yorkshire colliery records it is found much earlier and the singular form is more usual. In 1695, for example, William Goodall and Thomas Wood was the men that went into the bottom and gott by taske, Farnley. As a verb it signified that the sinking of a shaft was complete, presumably when the seam of coal had been successfully reached. An entry in the Farnley accounts makes it clear that this was yet another excuse for the miners to be given free drinks: 1719 ale at pit bottoming .
2) Land in the valley bottom.
1642 our manner is when our lambs are putte forthe, to lay them aboute ... the Dale bottome, Elmswell
c.1660 a little bottome or dale, Pickering. Very common as a minor place-name element and responsible as a result for the Yorkshire surnames Bottomley, Longbottom, Winterbottom.