Do you install the webmaster tool for each sub-domain seperatly or just on the main domain?
I installed it on the main domain and I see different data in different part of my Google analytics (the SEO part).
I install the webmaster for sub domain independently because it help me to see all the performance of sub domains one by one if we only add the main domain then it will be very difficult to understand things.
Yes, you can install webmaster tool for each sub domain separately. Do not create a new Google Analytics account for each sub domain's installation.
Google Analytics tracks one domain or sub domain by default. You need to modify GA's installation in order to allow proper tracking of your sub domains.
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