Often it is better to place your markers after initial image alignment as photoscan will estimate where your markers should go after you place each one in 2 images.
You can even align images and then build mesh based on sparse cloud and photoscan will estimate the position of each marker after you place it in 1 image.
Using either approach you can then whip through marker placement quickly by placing each marker in 1 or 2 images, then filter images by selected marker, and use page up and page down to flick through the images and photoscan will center each image on the expected marker location (with a little grey or blue (if you built the mesh already) icon) allowing you to place it quickly.