Generally, lithium batteries allegedly last longer when you don't "deep-cycle" them (IE, drain them mostly or fully). Putting them in the charging case when you're done using them would be the wisest thing to do, and then charge the case when you get back home.
Don't worry about it. When was the last time you actually wore out a battery...? I've never done so, and other than some freakish oddball internet report, nor have I ever really heard of anyone else managing, unless the battery in question was faulty.
The battery is meant to be used. You can be sure it has been plenty tested during development for its intended function. These things will work for years to come, and you'll either want to upgrade in the future because better buds came out, or you managed to lose one, or they became grubby and yucky after seeing much action inside your ear canals and thus eligible for retirement for that reason rather than the batteries wearing out...
Until a couple months ago my dad was still using my iPhone 4 which I originally bought in december of 2010 and which I used daily for three years before he got it. Same battery as when it was first made.