What you're going to need to do is rename your files to match the casava format and import them as the casava fromat. I've used the tutotial data found here for this examples.
Step 1: rename your files to match the following regex: .+_.+_R[12]_001.fastq.gz
Step 2: Upload your data to galaxy as a collection of type list
Step 3: Build the collection
Step 4: Import the collection
Let me know if you need any clarification on any of these steps.