Congressional budgeting used to run according to "regular order," in which each Department (Agriculture, Defense, Labor, etc) proposed a budget for the next year. Those went to the various committees overseeing each department (one for each Department in the House and the Senate). Each committee then negotiated their version of each budget. Then the respective House and Senate committees would get together and negotiate ("reconcile") a single budget for that Department. Once reconciled, the budgets would be formally approved first by the House (which has the power of the purse), then by the Senate. (Even here, there was a two-step process, in which each budget received a budget authorization [the maximum they could spend on each line item], then an appropriation [real money] which is usually less than appropriated)..After House and Senate approval, each Department's budget would go to the President for signature. Together, these 12 Departmental budgets comprised the total Federal budget. Once the budget was approved, money could not be moved around without going back to Congress for approval for the move.
Regular order was tossed aside under Obama. He allowed the last budget passed by the Bush administration to run out. When the deadline for appropriations came due, there was no normal budget. Instead, under the guise of a "continuing resolution" (which was originally a stopgap procedure), Congress just tossed in whatever they wanted, with no discipline or debate as to whether such-and-such a program was warranted. That's how Obama drove spending to new levels.
We desperately need to get back to regular order. Under that process, for example, Trump could get Defense funded, even if other parts of the government couldn't negotiate something in time. Breaking things apart allows better scrutiny.