The following command line tells BES to watch target.exe, and—when target.exe starts running—throttle its CPU usage so that target.exe will be only allowed to use CPU (100 − percentage) % at most:
Optionally, you can use an integer between 1 and 99 as percentage. If percentage is omitted or invalid, the last known valid percentage for target.exe is automatically used (if this is the first time to target target.exe, the default reduction 33% will be applied, unless percentage is specified). Note that, when started from command line, BES will Watch/Limit the target, not just Limit it.
The --minimize option, or -m for short, tells BES to start as minimized (sent to the system tray).
For the full list of command line options, start BES and see Help | Command Line Help.
You can use "pid:xxxx" just like a path, with most of the other options. Note that PID is not watched, just limited.
Start BES automatically when your OS boots
Create a shortcut to bes.exe in your Startup folder, where you can edit the properties of the shortcut and write your full command-line in "Shortcut | Target". Probably you’ll need to create/start that shortcut as Administrator.
To use the above-mentioned method, you may have to disable UAC and always log in as admin. If you do not want to do that, try this method instead: How To Use The Task Scheduler To Launch Programs Without UAC Prompts [tips thanks to João C; added 2017-09-02]. Also, there seems to be a way to disable UAC for a specific program (do some search).
Per-target Sleep/Awake Cycle
If targets have different paths, see above.
If you are dealing with two instances of the same exe and you want to use a per-process Sleep/Awake Cycle, try BES 1.7.5+, which understands "pid:xxxx" as a pseudo-path (see above). However, that may not work for you, perhaps because you don’t know the PIDs of your targets. So here is plan B: (1) copy bes.exe to a different folder. (2) Start BES A, check Options | Allow Multiple Instances, then Close BES. Do the same with BES B. (3) After that you can start BES A and BES B independently. Let BES A handle Process A and BES B handle Process B — you have to do this manually via GUI.
bes_1.7.6.zip
