Overlapping namespaces
If you are doing Drupal marketplace module research, and testing various options (which at this moment include this module and farhadhf's Commerce Marketplace) please keep in mind that machine name of farhadhf's module is exactly the same as this one, so you don't want to be testing both of them at the same time on the same site, as this would result in some unexpected behaviors (conflicting function names, database table names etc), quite probably including bringing your site down.
I would also advise against installing this module on the same site after trying out farhadhf's version before and then uninstalling it - information not verified in any way, but rumour has it that farhadhf's version does not uninstall cleanly, and its leftovers might again cause conflicts with this module. To be confirmed at some point, but I would suggest starting from a fresh install just in case.
Unmovable checkout panes
Commerce Marketplace introduces few new checkout panes - note that you don't want to manually move them around on the admin Checkout settings page, as this is done automatically by the module, based on several criteria (mainly number of stores you are ordering from and their available payment methods).
Store payment methods
When a payment method has any configuration options, it has to be configured for each relevant store before it can be used (even if such "configuration" means just saving an empty form), otherwise it will not be displayed in the Payment pane during the checkout process. Which essentially just means that only enabled and configured payment methods could be used for making payments.
Changing payment settings mid-order
When you are changing any marketplace-related payment settings (for example Send payments to value available on Marketplace Payments admin page, or enable/disable store payment methods, especially parallel/chained ones) please make sure that you do not have any active shopping carts (orders in either Shopping cart or any of Checkout statuses - especially those for which checkout pages might be automatically disabled by the system, like Checkout: Shipping or Checkout: Marketplace Review) (you can see them at Administration » Store » Orders » Shopping carts).
If you do, either delete them before changing those settings, or move them forward/backward in the checkout process to one of the "safe" checkout pages (those which won't be disabled after changing the settings).