Copy the script below and save it as "embed-cue.bat". Ensure that TAG.EXE is in a folder in PATH; I generally recommend people to put it in system32. This means you can then call TAG.EXE from anywhere without having to provide a path.
Then, simply drag the root folder (the folder that contains all you subfolders with FLACs) onto the batch file icon. The script will iterate through all folders, and when it finds a FLAC file called "<path>\<name>.flac" it will run Tag attempting to embed "<path>\<name>.cue" in to "<path>\<name>.flac".
CODE
FOR /R %1 %%G IN (*.flac) DO TAG.EXE -f "CUESHEET=%%~dpnG.cue" "%%G"
Please test this on some copies before running on your whole collection.