If they are donations to a proper registered charity, and if PayPal is the desired payment method, then you might find it easier to make a web page and put a few PayPal donation buttons on it. Alternatively make a form for the purpose. I've done this with Datasprings Dynamic Forms. The reason is really that it needs to be as quick and simply as possible for the person making the donation. Sending them through a store checkout isn't that great.
Note that the PayPal donations system is for legitimate charitable purposes only and they make sure that's what you are before they let you have the account.
If you are going to use the store, then a donation is just a product like any other. You can combine donations and product sales in a single cart, just make sure that your donation products have no shipping weight and your real products do. Then when someone buys only a donation, they get no shipping, but if they combine it with a real product, they get shipping for the product.
You'll also have to consider how you're going to handle donation receipts for the donors' tax purposes. You'll need to find out if a store receipt is sufficient and what information you need to gather and provide on it.
Regards
Rob