I hand quilt mostly with a hoop but sometimes without. Also, I mostly pin baste but will sometimes thread baste. Depends on the size of the quilt and how much weight I want to deal with. When I am sandwiching my quilts I use my cutting table to layer everything. I use big binder clips on the edges of the table. Put down the backing, smoothing and clamping to the table. Put down batting, smooth, clamp. Same with the top. I start in the middle of the quilt. Baste using pins or thread but in either case about a hand-width apart in all directions. Once that is complete I shift the whole sandwich working from the center out to the edges. I make sure that I have a basted section at one edge of the table, clamp it and continue the process. Sometimes can be a bit tedious if it's a large quilt but it works and I'm not crawling around on the floor or doing too much bending.
When I start quilting I begin in the center of the quilt and work out. If using a hoop the quilt is relatively loose in the hoop. Before starting to stitch I make sure the front and back are smooth. If there are puckers/ripples I pull that piece only (either the top or the bottom) a little tighter in the hoop. When finished with that section, follow the same process. I will certainly get the occassional pucker on the back but not too often. If I'm not using a hoop I simply follow the same process for smoothing. I find that having the basting, either pins or thread, about a hand-width apart (generally about 3-5 inches apart) the layers do not shift at all.
Hope this helps.