Onsite registration is signing up at the venue on the day rather than in advance, capturing details, payment and a badge in one step at the desk.
Checking in a pre-registered attendee is a lookup. Registering someone onsite means capturing their details, taking payment, and producing a badge, all while a line forms behind them. One onsite registration takes the time of several check-ins, which is why mixing both at one desk jams the entrance.
Signpost pre-registered attendees to self-service and keep onsite registration at a staffed desk away from the main flow. The staffed desk also absorbs the awkward cases, including name corrections, lost confirmations and people who think they registered and did not.
Will you accept onsite registration at all, at what price, and for which ticket types? Catering guarantees are already locked by then, and session capacity may be full. Plenty of events close onsite registration deliberately rather than scramble. Whatever you decide, publish it, because the alternative is your desk staff improvising under pressure.
Attendees can be added manually or imported in bulk from the admin side, and a badge prints at check-in from the attendee's record, so someone registered at the desk goes through the same badge flow as everyone else. See event check-in.