Linux (and POSIX compatible systems in general) inherit current process limits from existing processes when a new process is started (using
exec()). As a result, you would just need to change the limits for all existing processes that are already running on your system. The config files just define the values for the initial processes after the system has been booted and everything else inherits the current values of parent processes.
Why would you want to increase stack limit of everything? Do all your existing processes immediately require increased stack space for some reason?
If you actually need to change the limits of any given process after that process has already been started, you can do it with command
prlimit which uses kernel interface
int prlimit(pid_t pid, int resource, const struct rlimit *new_limit, struct rlimit *old_limit) behind the scenes. It requires
CAP_SYS_RESOURCE for many use cases so you often need to run that as
root in practice.