I just mean switch the transistor on/off. Use the low voltage from a micro-controller to switch on a larger voltage source to the leds. Am I understanding a transistor correctly? You can use it as a switch, yes?
If you look at Crutshaw's constant current circuit:
Use an extra NPN transistor (with base resistor) or N channel logic FET controlled by the MCU output.
Connect the emitter or source to 0V and connect the 10K bias resistor (R1) in the current source to the collector or drain, rather than directly to 0V.
Add anther 10K from switch transistor collector to LED power positive, to ensure the current source switches completely off when the transistor is off.
That would allow the current source to be enabled or disabled via the MCU output, as the transistor was switched on or off.
You could link all the 10K resistors from the different current sources to a single switch, or each controlled by a separate switch.
If the LED current is really critical, you may need to fine-tune the current sources to make up for component variations?
The current source can be easily made adjustable by replacing R3 with two series resistors, eg. a 10 Ohm plus a 4.7 Ohm, or 12 + 2.2 ohm for a smaller range.
Use the lower value at Q1 base end and connect a 100 Ohm preset resistor across it, with the transistor base connected to the preset wiper instead of the original resistor.
Definitely stay with a step-up converter, whether you use one or two cells. The adjustable output voltage means you can set it so not too much over the minimum voltage is lost across each current regulator, so wasted power will be minimised, and the regulator power loss is contact, no changes with battery state..
Using "bare" cells to get enough voltage means a significant change from full charge to flat, which could affect regulation and will cause more power loss in the current regulators, possibly affecting their stability due to temperature changes.