I have my own deals with a couple of airlines, can those fares show up in my flight search along with the normal ones?

Yes, in most cases they can, but it depends entirely on how your deal has been set up with the airline. Private or negotiated fares that have been filed electronically against your own agency credentials will usually come back in a search once those credentials are used for the request. They then sit in the results next to the normal published fares, and we can usually label them so your staff can see at a glance which fare is your own deal.

Where it gets harder is when an airline has given you a deal on paper, as a rate sheet or a spreadsheet or just an agreement in writing. There is nothing for a search to read in that case, so those fares cannot appear automatically. The practical options are to load them as a manual product that your staff select, or to keep selling them offline and record the booking in the system afterwards so your reporting stays complete. With that approach the rules and availability will not refresh on their own, so somebody has to keep them up to date.

It is also worth remembering that negotiated fares normally come with conditions, such as only certain routes, booking classes, cabins or travel dates. A search will only return your fare when the request actually matches those conditions, so a quote that falls outside the deal will quietly come back at the published price instead. Which fare sources you can switch on together can also depend on your plan and on what each supplier permits.

A good next step is to gather your airline agreements and check for each one whether the fare is filed against your own credentials or only given to you in writing, then send us that list so we can tell you which ones will show in search and which need handling another way.