if the boots didn't come with a pose set, have you got one for some other boots either aiko or v3,any mill3 figure.

now if you have a pose set for some boots, you are looking for the "hide feet"  inj. if you have one of them, then select M3, then double click the "hide feet", that might make the boot line up with his feet.

if not you will have to parent them from the "figure" drop-down menu, first make the feet and toes not visable (M3), then without conforming them(if you have conformed them then un-conform them) to m3 line them up as best you can,maybe scale adjust them too if they won't fit.Then when you are happy they are lined up, click the "figure" tab at the top of poser, and "set figure parent" (right/left foot for corasponding  boot) that should work too.