Can you see the battlefield in order to direct the battle? If so, then you can either directly communicate your orders to your chimera troops or otherwise communicate who the targets are.
Direct communication
Infrasound is apparently used by elephants to communicate over long distances – the low frequency acoustic waves travel further than the frequencies more familiar to us, particularly at certain times of day. You could broadcast a signal to all your troops in this manner, although I think communicating with specific units would be more tricky. Either you could send each unit a message sequentially (time-consuming) or send each unit a message on a slightly different frequency. The latter method is how modern radios work with EM waves, but discriminating between acoustic waves isn’t as easy. You’d have to engineer a type of chimera with an internal acoustic tuning organ, and then somehow manipulate that organ to tune each creature so that they would pay attention to a specific frequency.
Using a much higher frequency you can communicate more information over a given period of time, and in the case of ultrasound it’s much easier to envision a targeted beam of sound being sent at a specific chimera to command it to attack/move/wait… (This ‘beam’ could be created from as simple a set up as an emitting source and a funnel pointed in the right direction.)
In both of these situations I’m imagining the source of the signal is another bioengineered creature: either a full animal that you poke in a specific way to get it to emit the signal you want, or little more than an organ-on-a-stick that can be used to transmit your message over whatever frequency you’re using.
Communication of targets
‘Paint’ your targets (or the cover they are hiding behind) somehow in order to direct your chimera troops to attack the right people/locations.
Visual cues could include shining a focused ray of ultraviolet light across the battlefield. It would be visible to chimera troops engineered to see a wider spectrum than we do (as some insects can) but remain invisible to the naked human eye. (How to produce such a light ray using a biological mechanism is a bigger puzzle.)
Scent cues would be another possibility. I think in this case you’d need an in-between step in your attack plan: maybe insects that could be bioengineered to hone in on a particular type of person (some mosquitos have a preference for different blood types) or a particular material you know that the opposing troops will be wearing (armour?) or carrying (weaponry?). The chimera troops will then be trained/engineered to follow the targeting insects. Insects can be bred/engineered more quickly than full-grown chimeras, so if the battlefield conditions change next week you’ll only have to recalibrate your target vector, not the following troop unit.
I have to admit, these only go part way to fully controlling your chimera troops, and I haven't yet had inspiration for the targeting of a specific, high-value target.