Can I load my own special airline fares onto my portal so they show up next to the normal ones?

Yes in many setups, but it depends on the kind of deal you have and on the plan your portal is running. The important thing to understand is that not every special fare can be made to appear inside a live search, so it is worth checking before you build a campaign around one.

When an airline or a consolidator gives you a negotiated fare, it usually comes with a code or a contract number tied to your agency. That code can be attached to the search that goes out to the supplier, and the results then come back with your own price instead of the public one, so your staff and your customers see it in the normal list of flights. Other deals only exist as a rate sheet or an email from the airline, and those cannot be pulled into a live search at all. They have to be entered as a manual fare or quoted by hand, then recorded as a booking afterwards.

Be ready for a coded fare to appear less often than you expect. It will only show when the search matches the conditions of your agreement, so the route, the cabin, how far ahead the customer is booking and sometimes the passenger type all have to line up. When it does not appear, that is usually the contract rules doing their job rather than the website being broken. Whether your portal can also hold manually loaded fares depends on your plan, and who is allowed to sell a negotiated fare is always the airline's decision.

Gather your fare agreements together and ask your supplier which of them can be attached to a live search and which will have to be quoted by hand.