Is it possible (and advisable) to fill up a common online visa application form, but take appointments at separate visa application centers?
Each individual applying for Schengen visa has to make a separate application using the designated form (may vary slightly depending on the country involved), so to my mind the question of "common" online visa application form is moot. It is certainly possible for two individuals travelling together to apply at two different consulates if they are based in different cities.
Assuming that you and your husband are travelling to the same workshop and both of you will be attending it, both of you should fill the form and book VFS appointments based on your place of stay. Attach all the supporting documents (list based on German requirements but will vary depending on your destination country) with this form.
In the covering letter for this application, you can provide more details about your travel plans with regards to your spouse. Maybe something like:
I would like to submit that I am attending this workshop with my spouse X. My spouse is currently based in Y and has therefore applied for short stay visa at your consulate in Y.
or a similar variation mentioning common tickets/hotel reservations.