I recommend getting in touch with our QuickBooks Online Advanced Customer Success Team. They have the tools and resources available to share your screen and walk you through using Custom Fields in reports. Here's how to contact them:
It depends on the report you're running, custom fields filter report is limited to certain specific reports only. For example, Sales by Customer Detail Report.
Run the report and look for "Group by under Rows/Column" header. Only those reports, you should be able to filter it by custom fields. Click Customize and select Filter to customize multiple custom fields.