If you haven't already switch Veeqo on to manage stock we recommend that you switch this option on for each store. Veeqo is not designed to pull and push stock at the same time, therefore we recommend Veeqo is Master Of Stock for all your stores.
To enable Veeqo to control the stock levels of all your stores follow the Veeqo As Master Of Stock article.
Once Veeqo is controlling your stock you can either use Veeqo's Stock Take Feature to make sure your inventory is correct. Alternatively, you Update Stock In Bulk if you have this data stored somewhere else. If you have added Multiple Warehouses you will need to make sure that you have set the correct stock for each warehouse.