To switch from masonry to a grid of square thumbs please use a respective switch in ‘Theme Options’. You need to select ‘Grid’ and update the settings. Please click here to see a screenshot of these controls.
Also, what exactly do you mean by saying items don’t align properly when using the masonry layout? Can you please post a link so I could take a look and offer a solution?
I believe what’s happening here is that the third project in the screenshot you’ve posted has a thumbnail image with the dimensions that are too small to generate the needed 900×900 square thumb. Please try uploading an image that is at least 900x900px.
What you might not know is that you don’t need to resize images manually before uploading — WordPress automatically generates all the sizes of an image used in the currently active theme once you upload an image. So if your images’ size is in the range of 1500px (by the bigger side) to 3750px (by the bigger side), just upload them, and WP will automatically create copies in all the needed sizes. If you use pictures which are smaller than 1500px by the bigger size, they may turn out to display incorrectly. And if you use images that are bigger than 3750px by the bigger size, WP may have problems processing them (depending on your server).