A Company is any entity that has a forecast within Helm.
One of the easiest ways to differentiate between this term and an "Organization" (another term often used in Helm), is to think of them in relation to accounting system integrations and forecasts.
The entity you are connecting/forecasting for is the Company. The entity managing those connections/forecasts is the Organization.
Awesome Numbers Co. helps manage the numbers and forecasts of 20 clients. Awesome Numbers Co. is the Organization and each client is called a Company within Helm.
Conglomerate Inc. is a company with many related entities (operational and passive holding companies). It does forecasts for each. Conglomerate Inc. is the Organization and each entity with a forecast is considered a Company.