Go find a real Budgeting tool?
Seriously though, not trying to be a jerk, but NS' budgeting functionality is really, really, REALLY basic. You can get a Budget v Actual report with few or no variations, but that's about it.
As for best practices, assuming you're going to use it, most people I've worked with generally do whatever they need to prep the budget outside of NetSuite and then just use the budget import tool to bring it in once it's finalized.
Other than manual adjustments of numbers or being able to do amount +/- X% en masse, there's not much budget functionality within NetSuite itself once you have the numbers loaded.
It's a fine 'starter' budget tool if you've never really done any budgeting before, but most people I've encountered get frustrated with it pretty quickly once they start to want to do more involved stuff.