Hasn't the FY'09 budgets already been set?
The president signed the FY09 Defense Bills into law so DoD has Total Obligational Authority (TOA), but that does not mean they won't hold back on executing as planned. OSD puts a percentage of funding or certain items on withhold all the time and so does Dept of the Navy. Priorities and direction change all the time. What began as the President's Budget submit of FY09 was submitted to Congress in Feb 08 and sent to OSD from Navy in summer of 07. That's the last chance Navy had any options to manipulate it. Likewise, POM 10 budget data from the Navy is already at OSD and all hands are getting ready to have to rewicker that as well as PR 11 once direction is received. In a "normal" year (if there is such a thing), adjustments are made via an Omnibus reprogramming request mid Fiscal year to adjust for changes in service/OSD desires. In other words, OSD and the services can spend appropriated dollars for what was signed into law and released by Comptrollers at OSD and service level, but not for anything other than what was in the Congressional "Language" (except for certain "Below Threshold Reprogramming (BTR)" actions submitted to Comptrollers. OSD and services can also "not spend" appropriated dollars and either ask for reprogramming action from Congress (so they can spend it something else) or a rescission of funding (these are requests to not spend funds at all, usually when earmarks or "pork" items are included in a Defense Bill that the service does not want to execute typically because of the "tail" they bring with them*; Congress can respond to agree or direct funds be spent anyway).
So, yes, services or OSD can direct them to not spend according to the "budget". The next six months at very least will not be fun times to be in jobs associated with programming or budgeting (as if they are ever fun).
*Good example is "gift" of extra aircraft to a service that sometimes is written into language thanks to lobbying by a prime contractor wanting to keep a production line open. A new type/model/series or extra airframes necessitating new manning or facilities and logisitics has a large new "tail" and services will usually ask for rescission of the "gift". However, a gift of say, new C-103Js to USMC would be welcomed if they can replace older airframes with existing manning, facilities and logistics.
The Budget was signed into law, but there are processes to both increase the budget and decrease it.
I talked to how it can be manipulated to adjust priorities or reduced at request of services through OSD. I know of no "process" to increase the budget other than instances of Congressional Supplements that have been used in case of meeting unexpected war bills or other emergencies. I suppose you can categorize that as a "process" since it's been a regular occurence since GWOT began.