Although the recommended approach is specific to everyone's internal workflows, there are some general ways to tackle this problem.
The spent time to log must be assigned to one JIRA issue (of a JIRA project). If the time is not specific to an existent project, you can create a new one with a name like "Internal".
No matter in which project employees log their time, with ictime one is able (or must) select an activity type (depending on how the plugin is configured). The list of activity types is configurable by an administrator. Additional to that, ictime comes with a configurable checkbox option "No charge" and a text field for details, which can be checked by any user.
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