The auction buying (at the end of the auction - when bid is accepted) is evidently done by the winner. The auctioneer must have a paypal address saved in profile as the payment must have a destination. This way a winner user must see the paypal link in the auction details page with the amount bidded (plus shipment) to the auctioneer email.
In this example the auction has a shipment price of 50 USD and the winning bid is of 200USD:

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Therefore the final amount to pay is 250:

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Minimum increase can be set up from backend: default value and enable/disable the option of auctioneers setting up a different increase amount. The default number format is xxx.yy (. as separator and 2 decimals). The 2 decimals are recomended to keep as payment processors usually don't accept more decimals! As for the separators (decimal, thounds) depends on your server locale but can be changed in display using the number_format as modifier for smarty ({$dummy_amount|number_format:"3":".":" "} instead of string_format) and in programming using the number_format PHP method.

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Commission is tax you apply to a finished auction with winner (after bid acceptance). There can be various commissions to powersellers or verified users. The auctioneer "Doopz" has the 5% commission set. For a 200.00 USD winning bid the user "Doopz" is taxed 10USD (the 5% from 200). For another winned auction with the bid of 100USD he has to pay another 5USD. The total amount of commission sums to 15USD.

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