How to deploy machines with Apple IDs?

There are tradeoffs to any choice of Apple ID, but unless your personal Apple ID are tied to an Apple email, you can always re-name the Apple ID and change email, DOB, security questions, etc…

For pilot projects on iOS where the budget for apps is less than $1000, I usually recommend a personal account option when you don't have someone in the organization to manage email / fire up new corporate accounts.

If you do have control and desire to set up work Apple ID, then you should do that and keep the purchases on a work account per policy. This also is my primary recommendation for Macs since software costs are often higher and you are less likely to shuffle people through a Mac as opposed to an iPad or iPhone/iPod.

The process of discovering how you want to enable your people to work, who will be responsible for managing Apple ID / passwords is more valuable than any decision you actually make. Most decisions can be fixed / adjusted / changed if you find you choose unwisely. Just write up your plan, review it internally and go. You don't have to get everything right if you can loop back in 3 months and see how you did and adjust accordingly.

I would go to the seller of your Macs and see if they can advise you on how to deploy. If you haven't purchased yet, go to your local Apple store (if there is one) and talk with their Business Team. They help hundreds of groups like you navigate the path of using Apple at work. They don't charge for their time, have amazing resources if you stump them, and can hand you off to a local consultant if it's more economical to hire expertise if you have more money that time or training. A good consultant will guide you and inform so you can use Apple's planning guides to best effect.

Here's my TLDR advice:

1. Empower each Mac user to use their work email as their Apple ID and have no form of payment associated with these accounts.
2. Expect them to handle purchases / updates with a discretionary budget of gift cards that work provides, so you'll train them or get them to Apple for training so they can perform basic tasks / troubleshooting without needing your help. Treat one-off purchases like other things you use expense reports for and review all purchases quarterly or annually to see which apps you want everyone to be using.
3. Enroll your work in Apple's VPP program (even though it's designed for iOS - you will be forced to think about how to deploy apps and the resources there are worth your time to read / understand.) My guess is VPP will come to Macs this year with 10.9 - but that's wild speculation on my part.
4. Use one account to gift required apps to each user account if you find gift cards unworkable. Use this for purchases that are role-based as opposed to exploratory or one-off needs.
5. Consider enrolling in Joint Venture so Apple can provide your first line of help desk training and support in a business setting.