These are the steps I typically use to bootstrap an rclone install on Windows. My intentions with rclone are typically as a backup service, so this may not all be applicable to your use.

Create C:\Program Files\rclone.

Download rclone from http://rclone.org/downloads/ and unzip it to C:\Program Files\rclone.

Save this content as C:\Program Files\rclone\rclone.bat. 

SET RCLONE_ROOT_FOLDER_NAME=
SET RCLONE_FOLDER_NAME=

SET RCLONE_DEST=SomeBackupService:%RCLONE_ROOT_FOLDER_NAME%

cd "C:\program files\rclone"

for /f "tokens=1,2 delims=;" %%X in (sources.txt) do (
	echo %%X
	echo %%Y

	rclone.exe --config="./.rclone.conf" --exclude-from "excludes.txt" -v sync "%%X" %RCLONE_DEST%/%RCLONE_FOLDER_NAME%/%%Y
)

Set RCLONE_ROOT_FOLDER_NAME to the name of the bucket on your cloud service where you want backups to go. I typically use backups.

Set RCLONE_FOLDER_NAME to the name of this backup job (assuming you have multiple machines/jobs backing up to the same cloud service). So you may use something like backup1 or Office Computer or the date, or whatever suits your needs.

Create C:\Program Files\rclone\sources.txt file with a line for each source directory to backup, like so. 

C:\Users\admin\Desktop;Desktop

The path before the ; is the source path. After the ; is the path/bucket used by the cloud service.

Create C:\Program Files\rclone\excludes.txt with a line for each globally excluded pattern. 

"desktop.ini"
"Photo Booth Library"
".DS_Store"
".localized"

Run rclone.exe config to generate a config for that machine.

Move the generated config file from %USERPROFILE% to C:\Program Files\rclone.