Hi,
1. To set the post column to 3X3 go to Appearance -> Customize -> WP Portfolio Theme Options -> Custom CSS and paste the below CSS code then click on Save button.
.post-main .post {
width: 33.33%;
}
Also by upgrading to the WP Portfolio Pro you can set different column for post and have lots of features you will enjoy.
2. Sorry Can you please clarify your second question?
3. Sorry you can not reorganize the post for this you have to customize the theme code you have to hire a developer as this is a new feature to add in the theme.
Thank you for using our theme.