Sewing on velcro can be pretty tricky no matter what you put it on or what machine you use. You may need to sew between the rows and use a bigger needle - in your case a leather needle. It is just about impossible to sew through the sticky kind of velcro - try a needle lube product to keep the goo off the needle.
I wouldn't worry a whole lot about leaving that spring part down all the time I would worry more about forgetting to put it back down.