Yes, that is the whole point of a white label portal, so the site normally runs on your own domain name and carries your own agency name, logo and colours. You point the domain you already own at the portal, a security certificate is set up so the address shows as secure in the browser, and from then on it looks and behaves like a website your agency owns outright.
In most setups you can change the logo, the colour scheme, the homepage banner images, your contact details and your about us, terms and privacy pages. Booking confirmations, vouchers and invoices can usually carry your name and logo too, and be sent from an address on your own domain. How much of this you can edit yourself from the admin area, and how much needs to be done for you, depends on the plan you are on, so it is worth asking before you sign up rather than after.
Being honest about the limits, some things come from the airlines, hotels and suppliers and cannot be rebranded. Hotel photos, hotel descriptions, airline names, fare rules and baggage information all arrive from the supplier and will appear as they are written. If an airline or hotel sends its own message to the passenger it will carry their branding, and your payment page may show the name of the payment company handling the card, which is normal and customers expect it.
Before you go live, open the site on a phone as well as a desktop, make a test booking and look closely at the confirmation email, the voucher and the invoice to check your branding appears where you want it.