This depends on what kind of content the flash is. If it's a part of the design or framework and won't change very often, you can store it in your design directory and use the ezdesign-operator to retrieve it into a standard object element.
Otherwise you can store it pretty much anywhere in eZ, for instance in the media section. With the default installation the flash datatype should be available. When inserting it into a piece of content, use
<embed href="eznode://<node_id>" />
Consult this page: http://ez.no/doc/ez_publish/technical_manual/3_8/reference/xml_tags#object_embedding
If you don't like the default code that is generated you can override the template in use for the class type flash.
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