OK, so to reiterate - The needle must be oriented correctly for the machine. Steve gave some great tips on this. I'll add that on most "modern" (as in probably early 1900s to now) the last thread guide is also a clue. It will pull the thread to the side where the needle needs to thread from.
Most of the most common domestic machines of the same era will take a needle with a flat on the shank and that flat will be oriented to the opposite side of the last needle guide.
Needle in wrong is probably the most common reason for skipped stitches. Especially when this is coupled with threading the needle from the wrong direction.
Now, you CAN use a needle with a round shank IF it has the same other specifications of the proper needle. It must place the eye of the needle in exactly the same spot as the 130/705N or HAx1 or 15x1 needle. It really is simpler to just use the proper needle, since in this case it's the most common needle you will find or buy.
If you're having loops under the fabric, this is almost always top tension. One of 3 things has likely happened.
1. The machine is threaded wrong
2. In relation to the first point, the thread is not properly into the tension disks
3. I think this is most likely in your case - as Christy mentions - the presser foot lever is still up. Once we take the foot off, our perspective seems to change and we tend to leave it up by accident when Free motion quilting. The presser foot lever also affects the tension disks. If you leave it up, the tension disks are not putting tension on the thread and thread flies off the spool and leaves huge loops under the fabric. This will also cause skipped stitches because that loop that Steve mentioned earlier is of the wrong size, or it's so big it droops or flags and the hook tip can't catch it.
As for a darning foot vs "footless" stitching - to stitch without a foot, you probably need your fabric hooped. This is how my Singer user manuals have read whenever I've looked it up. The fabric needs to be taut and kept from flagging - which can cause skipped stitches. If you stitch with a darning foot, no hoop is needed. With a darning foot is way easier - I've tried both and stuck with the darning foot way of doing it.
The feed doesn't drop on the 99, so as Christy says - just put the feed to 0 and go. Many people - even
Leah Day - don't lower (even on machines that do lower) or cover their dogs and just set their stitch length to zero.