1. You use the Start Menu to start programs or access things not available in programs.
2. You use Control Panel to uninstall programs.
See <invalid hyperlink removed by admin> for reinforcement, but it's been this way since at least 1995 (Windows 95). <invalid hyperlink removed by admin> says: "Don't put shortcuts to the following items on the Start menu:" and mentions "program uninstallers", "web sites, and "help files" among some others.
Please only put a shortcut to the WinSCP program in the Start Menu, and if necessary, the two shortcuts to the key tools. If you are able to consolidate to just the WinSCP program, then you don't even need a WinSCP folder in the Start Menu, eliminating a "dry click" and making the program more accessible.