You cannot execute remote commands that require any input with WinSCP.
Please read documentation:
https://winscp.net/eng/docs/remote_command

The only option you have, is to store your password to a file; and redirect input to the application (if it's possible at all).

I am using the script to transfer files from the /cxc/logs folder on my Acme SBC to my local machine

I am facing issues to execute a daily command before synchronizing the folder
i need to run show version >>version.txt command on the remote server ,however the problem is this is a application level command ,not a shell command .

SO when i execute my script ,how can i define a 2nd level password

Eg ,when i SSH to the box i have 2 username and passwords
1st is for root
2nd is for application (like a enable password )

My sample script is like

open 2600LAB
call SHOW VERSION >>version.txt---- This only runs on the application level
synchronize "d:\logs\version.txt /cxc/logs/version.txt"
call cd /cxc/logs
call rm version.txt