For right now, the Batch Gift Entry tool is meant to be used for individual constituent gifts, rather than for organization gifts. The code for contact search in Batch Gift Entry explicitly excludes Organization Donor Proxies from the search results, which is why you're not seeing your organization show up in Batch.  This is because gifts from organizations are meant to be treated differently from gifts from individual constituents.  

For organization gifts, we recommend entering them individually by navigating to the Organization Account in question, scrolling to the Donations related list, and clicking any of the buttons for a new donation.  This will help tie the gift properly to the account in question.