Backup your web directory and store database.
Login to the admin panel and disable the cache as shown below:
Upload the app folder in Magento2 root directory:
Open Putty and Follow these commands:
Please find the link here to download the putty software http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html
Open the putty software, and click on RUN:
Enter all the credential details to connect it with the server. (Your credentials must be able to run php commands.)
a) Host Name (or IP address): enter your host name or IP address of your website.
b) Port: Enter the port number. It is provided with the ssh details when you create SFTP.
c) SSH: Select SSH radio button as shown in above screenshot.
d) Press Open
Enter your login username and password as prompted and you’ll be connected.
Navigate to your Magento root directory.
Run the command to enable the extension: php bin/magento setup:upgrade
Run command to flush the cache: php bin/magento cache:flush
Run reindex command: php bin/magento indexer:reindex
Once putty is completed, enter your site’s admin. Go to Sales/Configuration/Sales/Shipping Settings/Shipping Methods. SpeeDee should appear as an option.