In order to debug pxt-blockly in PXT, run the scripts/link-pxtblockly.sh which will link pxt-blockly under built/web/ and then instead of using index.html to debug, using blockly.html which will using the blockly uncompressed files instead of the bundled files in PXT.
To remove the link, there's a helper script that you can use as well scripts/unlink-pxtblockly.sh