Can I load my own contracted hotel rates into my travel agency software and sell them alongside the supplier ones?

Yes, most travel agency software lets you load rates you have contracted directly with a hotel and sell them next to the rates coming from your suppliers, though how you load them depends on your plan and on how many properties you have contracted.

The usual way is a simple upload. You prepare a sheet with the hotel, the room type, the dates, the rate and the cancellation rules you agreed with the property, and the system takes that in as your own inventory. Once it is in, your customer sees those rooms in the same search results as the supplier rooms, so they never have to look in two places. You also decide what happens when the same hotel comes from both your own contract and a supplier, whether your rate always wins or whether both are shown and the cheaper one sits on top.

It is worth being honest about the work behind it. Your own rates are yours to keep correct, so if the hotel changes its availability or closes out a date, you have to update that yourself, either in the system or by sending a fresh sheet. Supplier rates refresh on their own because the supplier sends them live, and your contracted ones do not. Agencies with only a few contracts manage this comfortably, and those with many usually give one person the job of keeping the rates current.

If you want to make a start, gather one signed contract with its rates, room types and cancellation terms, and ask for a single test property to be set up first, so you can see how it looks to a customer before you load the rest.