Model not centered on support

[Fed]

I'm new to 3d printing and was been messing with all kinds of settings. Apparently I broke something, because the models I'd like to print are no longer centered on the support material (picture 3). Another problem I'm running into, which may have to do with meshmixer, is that when I prepare to print this particular model it puts holes in the model where I added supports. The holes only show up when I prepare to print (pictures 2 and 1).

I tried "Help -> Reset all settings" but it didn't fix either issue.