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You can't. eBay has no provision for multi-package calculated shipping for a single item.
Best you can do is try to fudge it, if possible, by working out the range of costs for 1 box, multiply that by 3 to get range of costs for the 3 boxes, then work backwards in the USPS or FedEx or UPS (you didn't specify what carrier or service you were planning to use) rate tables, to see if there is a fictitious higher weight you can use along with a fixed handling fee that makes the numbers come out in the ballpark.
It rarely works at all, and if planning on offering multiple carriers or multiple services, becomes very messy and very unlikely to be at all usable.
Example: 3ea 14x12x12 5 pound boxes. USPS Priority Mail. Dimensional weight for zones 5-8 is 14x12x12/194 = 10.39 = 11 lb
zone 1&2 3 4 5 6 7 8
$ 7.41 8.42 9.37 21.54 27.81 33.87 39.76
Those are prices for 1 box, are horrible for zones 5-8 (due to dim weight) and unworkable. Forget Priority Mail and let's try Parcel Select:
zone 1&2 3 4 5 6 7 8
$ 7.41 8.42 9.37 10.65 16.14 18.46 21.02
3 x $ 22.23 25.26 28.11 31.95 48.42 55.38 63.06
18lb 14.30 18.30 21.49 31.08 41.74 47.78 55.49
+$8HF 22.30 26.30 29.49 39.98 49.74 55.78 63.49
So using a fictitious weight of 18lb plus an $8 handling fee produces a shipping charge approx equal to the total charge for 3 5 pound boxes, and works pretty well, but is too high by $8 for zone 5 (which is typical - there is something weird about USPS zone 5 rates and this has happened every time I try this)
Other weights from 10 to 17 pounds with different handling fee can also come close and one may be a bit better (goal is to never undercharge, not overcharge too much, and possibly refund any major overage)
If sizes and weights are higher this gets messier real fast and is less likely to work. Same with FedEx and UPS - much messier due to more difficult calculations and required use of dimensional weight.
That probably didn't help you much 
You can't. eBay has no provision for multi-package calculated shipping for a single item.
Best you can do is try to fudge it, if possible, by working out the range of costs for 1 box, multiply that by 3 to get range of costs for the 3 boxes, then work backwards in the USPS or FedEx or UPS (you didn't specify what carrier or service you were planning to use) rate tables, to see if there is a fictitious higher weight you can use along with a fixed handling fee that makes the numbers come out in the ballpark.
It rarely works at all, and if planning on offering multiple carriers or multiple services, becomes very messy and very unlikely to be at all usable.
Example: 3ea 14x12x12 5 pound boxes. USPS Priority Mail. Dimensional weight for zones 5-8 is 14x12x12/194 = 10.39 = 11 lb
zone 1&2 3 4 5 6 7 8
$ 7.41 8.42 9.37 21.54 27.81 33.87 39.76
Those are prices for 1 box, are horrible for zones 5-8 (due to dim weight) and unworkable. Forget Priority Mail and let's try Parcel Select:
zone 1&2 3 4 5 6 7 8
$ 7.41 8.42 9.37 10.65 16.14 18.46 21.02
3 x $ 22.23 25.26 28.11 31.95 48.42 55.38 63.06
18lb 14.30 18.30 21.49 31.08 41.74 47.78 55.49
+$8HF 22.30 26.30 29.49 39.98 49.74 55.78 63.49
So using a fictitious weight of 18lb plus an $8 handling fee produces a shipping charge approx equal to the total charge for 3 5 pound boxes, and works pretty well, but is too high by $8 for zone 5 (which is typical - there is something weird about USPS zone 5 rates and this has happened every time I try this)
Other weights from 10 to 17 pounds with different handling fee can also come close and one may be a bit better (goal is to never undercharge, not overcharge too much, and possibly refund any major overage)
If sizes and weights are higher this gets messier real fast and is less likely to work. Same with FedEx and UPS - much messier due to more difficult calculations and required use of dimensional weight.
That probably didn't help you much
