Charge it overnight if you prefer. You cannot "overcharge" it. When that message pops up, the phone has stopped charging, doesn't matter how much longer it remains plugged in.
Incidentally, I find that my phone really only goes to 100% if I charge it while the phone is off. If I charge it while the phone is on, it says 100% ... and I unplug it ... and two minutes later the phone is down to 97% or 98%.
Lithium ion batteries can generally be expected to last somewhere between 300 and 500 cycles before they start to lose capacity. One "cycle" is a full discharge and recharge of its maximum capacity, although not necessarily in one fell swoop. For example, let's say that you discharge your battery from 100 down to 50, then recharge to 100, then discharge back to 50. That is only one complete cycle (50 used the first time, recharged, plus 50 used the second time, recharged, equals 100).
In general, lithium ion batteries are better with multiple short charging sessions than they are with letting them drop to nothing and doing a full recharge; however, that sort of deliberate "full discharge until the phone turns itself off, followed by a full charge" should be done every 30-45 full charging cycles (which is not necessarily every 30-45 days you have it plugged in ... see above paragraph for what comprises a "cycle") in order to ensure the battery remains properly calibrated.
(One more thing ... the "full discharge/recharge every 30-45 cycles" recommendation is because, although lithium ion batteries don't have a "memory" in terms of losing capacity, they sometimes have a "memory" in terms of the power gauge ... thus the need for calibration every once-in-a-while.)