you can figure out how much budget for prospects pretty accurately by taking your draft positions and looking up last year's bonuses paid for those slots. Sometimes look back at 2-3 drafts if something seems out of whack (like a lower pick getting more bonus than a higher one, which can happen). So, if you have pick Round 1 - Pick 17 (1/17), see what 1/17 got last year, and so on.
You can get in a pickle if you say "each year I budget $6mm for draft picks" when this year you have 3 comp picks at the end of Round 1, so be sure to account for the number of picks you're likely to have and their slots.
Then, if you're gonna take a flyer on a hard-to-sign guy in a later round like 2-5, that guy is still gonna want high-pick money, so you'll have to budget for it if taking such a flyer.
In-season budgets can be worked around, so I don't feel much need to save too much budget for in-season trades. You can work out the money as part of the trade to make it work for both teams...I don't often see budget constraints prohibiting a trade. A bigger problem - though not in the grand scheme of things - is when your budget is tight and you want to promote a guy or sign someone to your minors cuz of injury. If you sign a couple extra inactive pitchers and maybe a SS or two who can play anywhere then not much need to save budget to fix minors during the season.
Also, if you're planning to sign a bunch of IFAs, even just as DITR lottery tickets, each of these guys gets a salary too, so you'll need the payroll room for it. Rookie League earns about $8k, so allocating $80k is enough for 10 IFAs salary-wise. In total, it seems about $300k gets you through all the incidental payroll-related moves during a season. Exception would be going from AAA to ML, which each cost about $275k in salary bump to big-league minimum.
One last note which cost me about $3mm on accident and I'll never screw up again: if you bring up guys to the majors when rosters expand just for the experience, be sure to move them back down before the end of the WS, else they make the big-league minimum next year when you have them back at AAA!!!!