First of all, you can represent each of your fixed pick up sites as a separate user-defined shipping method in Ecwid control panel → System Settings → Shipping → User-defined Methods. So, you should have as many user defined shipping methods as the number of pickup places you have, each method named after the place (customers see those names on checkout, so be as verbose as possible with naming them). Make sure, the weight limits of those methods are big enough to allow an order you can dream of.
The rates formula depends on how exactly the rates for each pickup site are comprised, but generally the shipping rate of a user defined shipping method consists of per order rate, per item rate multiplied by the number of items in a particular order, and a per weight unit rate multiplied by the order's weight. If your cost to deliver an order to the pickup site is 0, just keep all the rates at 0.00, if there is a fixed flat rate, put it into the per order column, and so on. Please provide me with the details of how the costs are calculated, if you need more help with that.
The destination zones are not quite necessary for this setup - if you just add as many shipping methods as the pickup sites you've got and you put the rate for each of them into the 'The World' row, each customer will see the whole list of the pickup sites and will be able to choose any single one of them, without limitations. The destination zones may help to limit the availability of any single pickup site in your setup to a particular geographic area. So, if you have a pickup site, let's put it roughly, in California and wouldn't like to offer it to new-yorkers, you should limit the availability of that particular pickup site (which equals to 1 user-defined shipping method in the proposed setup) to some destination zone. But if you want to totally allow your customers to choose from the entire list of pickup sites, you don't need zones.
A destination zone is defined with countries, states and zipcodes, and the customer's address must match all the given parameters of the zone (i.e. if you have states and zipcodes in your definition of the zone, address must include one of those states AND at the same time one of those zipcodes). If you are going to limit the availability of a pickup site to cities or neighborhoods, you will stil have to operate with zipcodes of those places.
Once you have set up a destination zone, where some particular pickup site is available, you need to apply that zone to the rates you have set for the shipping method that represents this pickup site. Simply go to the Ecwid control panel → System Settings → Shipping → User-defined Methods again, and under the tab representing the particular pickup site, change the zone in the dropdown from 'The World' to the one you created for this site. With pickup sites bound to zones, your customers will see a limited set of pickup sites available, based on the match of their shipping address to the zones you created for those sites.
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