You might think about using a relational database.
This can be structured as a number of seperate 'tables', each
containing a type of 'thing' - in your case, you could have a table of
'users', with their details; and a table of 'markers', each with its
location details (that are searchable) and a cross-ref
to its owner/author.
Want a list of all a user's markers? Easy
Want a list of everyones markers between certain lat/longs? Easy
Want to add something new, like polygons? Easy - add another table

cheers, Ross K

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