I would have to agree with the previous poster:
From my understanding supply=demand so I would stick with offering both sides at each feed
Although Tracy advocates single-sided feeding to start off (which I did happily), even she assumes most people will move to double-sided. In the first book on p.116 she says it usually happens by the time the baby is around 12lbs. If a mother has any concerns about supply then the LLL would be very adamant that double-sided feeding is best (actually they are fans of it for everyone). I would say your LO has naturally shown he is ready to move to 2 -sided.
Can I just question an assumption you have:
given my boobs an extra half hour to fill up again after the 6pm feed
Boobs actually don't fill up as you describe nor do they store the milk from feed to feed. The milk is manufactured
during the feed - a very small initial amount is held in the ducts but it really isn't much (and was recently discovered to be even less than we had previously thought - research done by Peter Hartmann in Aus. in 2005).
If the milk was held in the breasts as many imagine then breast size would be a much bigger factor in successful breastfeeding. Some engorgement is caused by the milk ducts becoming distended but this is a small amount of what your baby will actually take in during the feed. Many women experience no engorgement at all between feeds. If breasts did 'fill up' then the blanket advice given by medical professionals in the 1970s (certainly in the UK) of everyone starting on 4 hr cycle for newborns wouldn't have had the devastating effect that it did on people's supply and ability to breastfeed.
Breasts are all about supply and demand and what's been demanding of them previously as the pp said. Your breasts are accustomed to manufacturing less later in the day because that's what has been asked of them but also because that's the way pretty much everyone's supply works. It's why cluster feeding in the evening is a natural pattern for very young babies. It explains why after a good night's sleep our supply is back up - breasts flag as the day goes on!
I'm hoping that by pumping that bedtime feed I'll be able to increase my supply at that time of night.
You are right to think that by increasing demand you can adjust your supply but a pump isn't exact in reproducing the baby's milking action (the wave like motion on the underside of the nipple) so it doesn't do the job exactly and not everyone is able to solve the problem of the evening supply dip.
I've been pumping the 6pm feed and feeding it to DS by bottle (to teach him to take bottle too - it's early days and it's still a battle )
If your evening supply is an area of concern then I think it might make more sense for you to try to move your pumping earlier in the day and having as much natural feeding later on (i.e. with his milking action.)
I know this is all extra hard for you because you are concerned about his bobbing on and off which doesn't make things easy but his feeding is still more effective than a pump - you could always offer the breast first and then top up with what you've expressed earlier (which you would need to do initially anyway if you did make the move)!
I should also mention that you are getting a lot when you pump !! 200ml is a heck of a lot. It's not uncommon for mums to find that pumping output does decrease as their babies get older and their breasts are more intelligent/ used to baby's milking action. Some mega-pumpers have no change but some people do settle down at around 2-4oz especially around the 3/4 months mark.
It's very normal to have slightly different supply in each breast - infact it's rare to have exactly the same. You could certainly try and pump more on the right after a feed.
I've said a lot of different things there - In summary!!!:
Certainly pump to increase supply but also understand the 'importance' of natural feeding to regulate supply.
You're normal with regards to the evening dip and uneven boobs.
I would stick with double-sided rather than attempt to revert back.
Do ask someone about the bobbing if you do feel it's really making a difference to life (I know I'm a nag)
Have you found someone to help with the reflux?
It sounds as though you are working so so hard to make this a success. I know your LO will reap the benefits even if some days feel tough. I do think your first stop is trying to get to the root of his bobbing and then the supply questions may fall into place.