Shipping is one of your LARGEST costs to online selling!
So it pays to take some time to learn how it works. hate to say it, but if it is too complicated then perhaps one needs to reconsider selling?
As you have discovered messing up on anticipated size & weight can cost you a bunch and perhaps wipe out all profits. Continue to do that and your selling career will be short! 
But with some patience and persistence one can learn this new 'language!'
First step is to learn how to use eBay's shipping calculator. I use it and usually measure my items and add 2-4-in to each dimension to give room for packaging and cushioning. I have a scale so I can weigh each item and have found I can safely add 8-oz to most of those weights to account for the box and packing. Often print my labels using the 'estimated' weight & size and have not had a miss yet - but it does take some practice to get there.
@corvettestainless wrote:measure my items and add 2-4-in to each dimension to give room for packaging and cushioning. I have a scale so I can weigh each item and have found I can safely add 8-oz to most of those weights to account for the box and packing. Often print my labels using the 'estimated' weight & size and have not had a miss yet
This is how NOT to do it. Don't 'add 'fluff' to your dimensions or weight. 8 oz. is the difference between paying $10 on a 2lb+ package and $16 on a 3lb package. 2-4" could be the difference between paying $20 (12x12x12) and $55 (14x14x14).
Find the box, weigh the item with the box with whatever packing you are going to 'safely' pack it in.
Well maybe some people want to skimp on the dimensions and padding/packaging to save? Those added dimensions and weights are reasonable assumptions to make sure items are protected. I'd rather see my items get delivered in good shape and avoid SNADs when they experience rough handling.
Using the method suggested gives a starting point when using the shipping calculator and if the cost is prohibitive, then one looks for reasons why (too many inches or too much weight) and then can evaluate IF they think they can skimp on those two and still have the item delivered safely. Finding the EXACT box and weigh can be the best way especially if one is using calculated shipping, but the method I have used for years works for me and I have NEVER paid more than I need to. I also have to think that the frequent issues of "I sent the wrong package to the buyer" is a result of prepackaged items (one box looks the same as another?).
Paying $16 on a 3-lb package might be out of line because you might be able to use cubic shipping rates or FRB/RRB that is much cheaper. But we could do hypothetically jousting on this forever. Methods suggested requires use of a scale, tape measure and shipping calculator and is a darn sight better than the 'nothing' or 'eyeball method' OP was using.
So a smart seller might have a stack of pre-assembled FRBs and RRBs sitting next to their table when measuring and listing as a method to see which of those might work and then use the calculator to get the best 'fit'. Have never had many boxes and packing exceed 8-ounces unless it is a fragile item that needs double boxing. But hey, if the cost looks out of line one can always look for ways to skimp on packaging and damage prevention!
BTW - rates for a 2# priority Box to zone 8 is $10.86 versus $15.28 for a 3# Priority Box to zone 8. A difference of $4.42, not $6. A seller would need to evaluate if the additional 4.42 was worth the cost in protection of what they shipped and not just shoot for the smallest lightest package they can find and "hope" the item doesn't get damaged.
I have great success with my methods and design my packages to be able to take a tumble off of the top flight of a stairs onto a concrete floor and still survive. NEVER have I received a complaint about shipping costs or that items were damaged in shipping.
But hey, everyone is free to make their own evaluations and skim on packaging and protection of the items they ship!
