The 3% figure is wrong for hotels. Online travel agency commissions on hotel bookings generally run in the mid-teens to low twenties as a percentage of the room rate, with the exact number set in your contract with each site and varying by whether you buy into their preferred or visibility programs. Confirm the rate in writing with each channel before you model it, and treat it as a real cost of revenue, not a rounding error.
On the software, those are usually two bills. A property management system, the PMS, is the software that holds your reservations, room assignments, folios and nightly close. A channel manager is the piece that pushes your rates and availability out to the booking sites and pulls reservations back in, so you don't oversell the same room twice. Small-property PMS pricing is often quoted per room per month, commonly in the range of a few dollars to around fifteen, or as a flat monthly fee, and channel managers frequently sit in the low hundreds a month. Some vendors bundle both plus a booking engine for your own website. Ask for the total including setup, and ask whether they charge per reservation on top.
Card processing is the bill people forget. Somewhere around 2 to 3% of everything you collect goes to the processor, and on a hotel that's most of your revenue.
The other thing to sort out early is your transient occupancy or lodging tax registration, which is set at the state, county or city level and differs a lot between them, so check with the local taxing authority for your specific address rather than assuming it works the way it does one town over.
