As it happens, I do have recent experience checking in large items like this on Emirates. Provided your item is both within the 300cm size limit and does not exceed the weight limit for a single item (32kg, from memory - but you'd better check), it is straightforward. The exact procedure may vary with the airports involved, but in general you present yourself and your item at the check-in desk, and they'll either take it there, or weigh and label it then ask you to take it to the oversize items counter, or ask to you take it to the oversize counter for weighing and labelling. In my case (at SYD), they weighed and labelled everything at the standard check-in desk, then asked me to put the oversize items in a special cage set up at the exit of the Emirates check-in area.
At the other end, your oversize item will probably appear* at the special oversize/fragile item delivery area, which is often in a distant corner of the baggage hall, and sometimes rather well hidden.
Note that the weight limit for a single item is absolute: it is not a matter of paying an excess charge; they simply won't accept an item over 32kg (or whatever it is).
*unless, of course, you are waiting at the oversize delivery area, in which case your item will appear on the regular carousel at the other end of the baggage hall.