By Law, the president must prepare and submit his proposed budget by integrating and prioritizing inputs from all the cabinet agencies. He starts this in Sept-Dec of 2009, and sends it to Congress in Jan 2010.
Congress receives the President's budget proposal, then holds lots of hearings to review, adjust and agree on an overall budget. They pass the resulting budget resolution, sometime in late spring or summer of 2010. This establishes the levels of money that agencies can plan for. They are now 1/3 of the way done. No money can be spent yet.
For discretionary programs (not entitlements) Congress then passes legislation authorizing expenditures for various programs up to the agreed budget limits, providing the legal basis for the Government to spend the Public treasure. They must then pass appropriations bills (usually about 20, separated out by Agency, such as DoD, Interior, etc.). The appropriation (which can be less than the authorization amount) actually gives the money to the Agency to spend. This is supposed to happen in Aug or Sept of 2010, so that the funds have been budgeted, authorized, and appropriated in advance of the start of the 2011 FY on Oct 1, 2010.
I left out the parts about reconciliation between House and Senate versions, Presidential vetoes, and other gotchas, but the process is specified by Public Law passed in 1921, and has been mostly followed for most of our modern history. The continuing resolution is supposed to be an emergency measure only used for short periods when some emergency delays the completion of the process by the Oct 1 start date of a FY.
The current mess we are suffering through now regarding FY 2011 spending is the result of the complete abdication by the Democrats in control at the time, of the fundamental requirements of our federal government expenditure system. This began in early 2010 and continued throughout the campaign season, out of Democratic fear of public scrutiny of their spending plans in advance of the Nov 2010 elections. Shameful.