This is just begging for to 145 St fowming, but I'm NOT taking the bait !
My first thought was to find a way to turn the in Manhattan, but since that would probably mean 34 St-Herald Sq or 34 St-Penn Station, I decided that it was more trouble than it was worth...I'll follow the K.I.S.S. rule:
terminates at Marcy Av, Myrtle Av, or Broadway Jct. riders in Brooklyn are advised to transfer to the at Broadway Jct.
uptown trains stop on the local track at W 4 St (or to avoid the wheel detectors, they can run local all the way to 34 St)
select Manhattan-bound trains terminate at Whitehall St
select Queens-bound trains run via the line from Jay St to W 4 St
select Manhattan-bound trains terminate at either Myrtle Av or Marcy Av
Note: I decided to try to keep trains as close as possible to their normal routes, because as Trainmaster5 said, it's a hassle to return the trains from faraway places when normal service resumes. For example, if the terminated at 57 St/7 Av via the line, there would be no available trains on the normal route for a while after the service change ends, while crews try desperately to transport the equipment back to the 6 Av/Concourse lines.