the U3S will auto cycle through a maximum of 16x 2minute operational slots in sequence. You have to re--set the default from 3 slots (TxS). You can choose the transmission mode (WSPR) and frequency different for each slot but you must match the LPF with the frequency as well. It is possible for some bands to re-use the the same LPF but you have to be able to check the harmonic suppression is suitable.
It is not recommended to use the WSPR double frequency modes for normal and multiband operation.
For 'silent slots' you can use the 'RX' mode.
You need to set and allow a 2 minute gap for CAL update at the end of a full sequence so you need to calculate and set your FRAME carefully, i/e 16 active slots plus CAL = 34 minutes repeat cycle, but then you get long periods of nothing happening so I tend to limit my operational slots to 9 (=18 minutes) plus CAL (2 minutes) and FRAME at 20 minutes so it all repeats at 40 and 60 minutes.
Hope this all makes sense.
I use an LDG Z11 auto atu but it does need at least 500mW to auto set, so you may have to run you U3S PA at higher than 5v (say 10v) to get sifficient power without resorting to the compllcation of an external PA and re-wiring of the LPF paths.