Where did you get these iron on transfers and what are they like? I don't think I have ever worked with iron on transfers, so I'm trying to wrap my head around what you have. Are they large, small, thick embroidery patches like boy scout badges, or .....? Does the package say anything about stitching? Some fusibles are made to be stitched through but others are not. The ones that are not made for stitching will gum up your needle quickly. Some people have sewn through them anyway, periodically cleaning their needle with (I think) a swab of rubbing alcohol.
What is the final use of the quilt you are making? Will it hang on a wall, lay on a bed, or be a utility quilt for snuggling? All that info helps. :-)