For aesthetic reasons, it would be nice to have both working transfer tracks and also not having to empty the queue to change the number of coaster trains running. However, as a practical matter, there is no need at all for either of these. Using the transfer track would consume at least as much time as you lose closing the ride and emptying the queue, and in either case the ride isn't shut down long enough to make a real difference in your income. Besides, if you design the coaster correctly, the need to change the number of trains running should never arise.
A coaster has a maximum number of trains it CAN run, which is based on track design, and a maximum is SHOULD run, which is based on the coaster's popularity. When building a coaster, you should always attempt to make these 2 numbers be equal. If you do this, then there's never any need to change the number of trains.
A properly optimized track design will have a train entering the station only a few seconds after the train ahead of it leaves the station. This is what maximizes customer throughput. To do this, start by always using a station where you enter on 1 side and exit on the other side, and the exit gate should be centered on where the coaster stops in the station. Then set the station wait times to a minimum of 5 seconds and a maximum of 28 seconds, select "Full Load", and check the "Don't block station" checkbox. Having done this, you next have to decide on how many trains you'll have, usually 2 or 3. For each train, the ride duration has to be about 30 seconds, so for 3 trains you need a ride duration of about 90-100 seconds with block sections every 30-35 seconds along the track, and of course 2 block sections on the back of the station for trains #2 and #3 to start on. 30 seconds is about the average time for a train to do 2 vertical track elements (loops, airtime hills, helices, etc.) so that tells you where to put the mid-course block sections.
With those parameters in mind, it's up to you to design the track so that the ride's stats and prestige appeal to enough peeps to keep the queue full, which will ensure each train gets a full load in 30 seconds. For a coaster big enough to run 3 trains, this often means tailoring the ride's EFN (excitement, fear, and nausea) ratings to appeal to a different audience than other coasters in the park with similar prestige. Which means you have to study peep demographics to know what they all like.
