I’m afraid there is no simple answer to your question…just to give you a quick resume of my background, my previous job involved running my (now sadly deceased) ex-gaffer’s wagon as my own, and I was paid part-profit share, so I came up against this one on a fairly regular basis.I’m now working as a “proper” employed driver for a Hull-based firm which does a good chunk of spot-hire work, as a means of taking time out and saving some cash before finally getting 'round to “going it alone”. 
The vast majority of container jobs are paid as a “round trip”, so you are paid to go to the delivery point, tip, and return to the place of restitution - often the same port which the box came out of. You also get demurrage after a certain amount of time - generally 3hrs for a 20ft and 4hrs for a 40ft, although that varies between firms and shipping lines.
So in theory if you carry 2x20ft then you are getting 'round trip on both, which increases the attraction of both the newer splitting-skeletals, and wagon and drag (which is what I want to run…hence the need to get more money up in order to invest in what will be a pretty specialist rig)
In practice, however, it’s not quite that simple, since the shipping lines are not daft…when the job is invoiced they usually want POD which includes the delivering vehicle’s registration. From their point of view, there is no way on this earth that it is reasonable to pay full double-bubble round trip when they know ■■■■ well that both boxes were on the same trailer/rig and therefore you didn’t actually do twice the mileage. What therefore normally happens is that the rate for both boxes is negotiated as one job, and a middle ground is agreed.
That is not to say that a certain amount of scheming and skullduggery doesn’t go on on the hauliers’ part - and who can blame them given how little money there is to be made in the first place!
Classic examples include trying to sneak PODs through with the wrong reg. on…invoicing for the 2 jobs a few days apart in the hope that the second one will “slip through the net”…booking one or both of the boxes into a storage yard and then pulling “different” and “damaged” empty boxes out again so as to turn the whole thing into 2 jobs (happens with single 20fts and 40fts etc as well - and 9 times out of 10 the yard boys will “find something wrong” with the boxes and let you keep them on…and so on. You get the gist.
Of course, if you can carry 2x20ft boxes for 2 different shipping lines then you’re laughing…but even sole-shipper type contract work pays far more with the two boxes, to the extent that one particular Southampton-based dedicated haulier guarantees it’s subbies at least £1550 p/w for a standard artic (which is just about enough to break even and have a pint on the way home), against £2000 for a wagon-and-drag. To put that into perspective, when I last did the costings I worked out that I could run a w/d for 8p/mile less, based on similar aged/priced power units, with the whole set-up running on 6 axles.
Bet you wished you hadn’t asked now!!!