In general, no, it does not matter. There are a FEW exceptions or, more correctly, factors to consider.
First, case ventilation fans should not be connected to CPU_FAN or CPU_OPT headers, but you already are doing that right. IF your mobo has a header with the label PWR_FAN, do not use it. That is a special-purpose header intended for a way to connect special leads from a PSU to the mobo solely to allow the mobo to display the speed of the fan inside the PSU. It's not for case fans.
SOME mobos have several options available for which temperature sensor is used for each fan header. The common basic system has only two temperature sensors. One is built into the CPU chip itself and automatically is used to guide the control system on the CPU _FAN (and possibly a CPU_OPT header). The other, built into the mobo by its maker, is used to guide all the CHA_FAN or SYS_FAN headers. On such a system, all the CHA_FAN etc. headers are equivalent, unless you customize their controls. But come fancier mobos also include one or two additional temperature sensors and allow you, for EACH CHA_FAN or SYS_FAN header, to choose which temperature sensor is user to guide each header. IF your mobo has such a system you can choose to make those headers somewhat different in that way. AND, if you have such a system, check it: many of them are set by default to use the CPU internal sensor for all fan control, whereas the case ventilation fans ought to be guided by a mobo sensor.