Custom field values can be set on a per-project and/or per-rule basis in your JEMHCloud profile, where they are called Custom field defaults.
Go into your profile and configure it by clicking the small cog beside it 
. Go into the Project Mappings view. You can either configure the new Custom Field Default to be at the default project mapping resulting in your other mappings inheriting it, or you can configure it to only be in one of your non-default project mappings.
Click the little cog beside the project mapping you've elected. Go into the Issue tab and click the Edit button found towards the top right. Scroll down until you see the Custom field defaults section.
Setting a static value
The simplest way to set a custom field is by passing a static text-format value. Find the desired custom field from the list. Ensure that the drop-down at the end of the row is set to Text, and enter a value to be used for this project mapping/rule.
Once a value has been entered, you can then select when this value should be set (issue creation, issue comment, both). Finally, submit the form to save your changes.
Setting a dynamic value
If you wish to set a value that it dynamic (changes depending on other variables), see Set a dynamic custom field value for more information.