Congressional committees make changes to the President's proposed budget and bill language. (The actual physical paper bill has material inserted or deleted in longhand, hence the term "markup." These changes are reflected in printed draft versions of the bill.) Markups reflect decisions made at various stages of the processing of a bill through Congress and its committees.
Markups are Congressional cuts or additions. They include attempts at changing or restricting other laws or Administration policy through "riders," or additions that have nothing to do with funds but for which the appropriations bill is a convenient vehicle. Appropriations bills must be acted upon every year, and provide an annually repeating basis for action using Congress' only direct tool; more relevant legislation may not come up for action for a decade or longer.
Cuts or reductions in funding are obviously directly related to funding, but they may be motivated by other than simple economy:
"Across the board" cuts are used when there is no specific item to be cut but a reduction is needed either to meet some target or to meet the target while providing increases for specific items, such as "earmarks" (which specify funding for a specific item so it is funded).
Appropriations committees also provide instructions to the agency in the reports on the bill without affecting funding. These instructions make clear to agency heads and operating managers what Congress expects.
There must a record of what Congress does and why. Without such a record it would be difficult to conduct business. Even if Congress were to approve the budget as submitted by the President, there has to be a record of the approval. But Congress has its own ideas as to what is appropriate, and reflects this by marking up, or changing, proposed legislation.
Agency and Operating Official Actions
An agency has a keen interest in the markups and will attempt to influence the process. Operating component officials may be involved in this process, especially if riders or other policy affecting changes are being considered in areas related to the operating officials' expertise.
Any time between the hearings and the votes on the bill.
Documents and Links
The printed copies of the marked up bills are generally available. Reproduced copies of handwritten changes may circulate to selected people as actions take place. There are no links that have timely information other than subscription services.