Hi flowerfairy - I kept mice (males and females) for over ten years in the past and had to use Baytril occasionally mainly due to the fact that mice (like rats) suffer from the Mycoplasma Pulmonis bacteria which can affect their respiratory tract and lungs. They are born with it. I probably have various historic posts on here relating to mice but wanted to answer your point regarding the dosing of Baytril and the best way to do that.
After years of using Baytril with barely any positive outcome, I asked my vet about whether he was actually dosing it properly and we came to the decision that the dose was not being given often enough. So rather than the universal "one drop on food" theory, I did one drop on a tasty piece of food I knew the mouse liked and would eat THREE times daily, spaced apart morning, afternoon and late evening. This proved to be more effective. Mice, like all small rodents have fast metabolism so the spaced dosing worked better, I found.
Some mice will carry on regardless with some acute breathing issues while some will become more chronic with it. Those are the ones who you should concentrate on the most to help them along. Not easy I know when you have more mice running over to see what`s for eating!
I never did full cage cleans with my mice or my dwarf hamsters or used cleaning agents. I found these to be troublesome around small creatures who are prone to this condition and wiping down the areas daily with a wet kitchen towel and removing the wheel and the food dishes to clean those in good old washing up liquid was fine. Mice scent a lot and smell more, I know, but over cleaning too can cause more stress than is necessary.
I had a large Gabber wire cage with multiple females in it with hammocks, ramps, etc....and cleaned around the cage with the mice still inside! Then again, I knew their characters so they stayed away from the main doors when I was wiping around the cage floors. They do get used to this.
On the best food to `lace`with Baytril. My favourite was half a thumbnail sized piece of rich tea biscuit, dip it in water until it`s soft (but not soggy) add the baytril and let it absorb into the moist biscuit on a plate. Once it sinks into the biscuit, offer it to the mouse (but try and be sneaky and offer it when she`s mooching about for a tit-bit! Or you can dose them all at the same time. It won`t work all the time but baytril does taste foul.
* Please ask your vet about this
before proceeding though because my vet was quite open to suggestion* Your vet may not be.