Yes, STM lenses do allow manual focusing override after auto-focus has locked (indicated by camera beep, which can be turned off in camera options). STM lenses focus should not be adjusted manually when in AI-Servo focusing mode (i.e. when the lens is constantly seeking for focus), nor before engaging AF when the lens is switched to AF mode. An USM lens would allow manual focusing also during AI-Servo auto-focusing.
The viewfinder on the Canon T5i is not optimized for manual focusingnot optimized for manual focusing; a good alternative is to use magnification in Live View.