First of all, don't ask your HRIS vendor for customized programming until you've determined that what you're asking for isn't going to be on the next release of the software. Check with the users group to see if there are other companies looking for similar programming; this is where the vendors get 90% of their ideas for software enhancements and if other companies need it, you'll probably see it on your next update.
Updates to the software generally fall into two categories: minor and major. Minor updates generally are included as part of your original purchase agreement and come within a short period after implementation. Major upgrades will involve some cost on your part, and can be as much as 20% of the cost of your original system software, depending on the types of updates available.
Don't automatically jump to the next update unless necessary, but keep in mind that for most vendors, you can't skip more than two or three updates without doing another full implementation.
You should also budget annually for equipment upgrades such as workstations (especially if it was too much to bite off in the original implementation), data storage, interactive media (e.g., voice response, web-based data entry) and third-party vendor networking.