If you have illustrator and are designing logos, you'd do best to learn to design them there. But as long as you're working with vectors only in PS you should be okay.
As for me, if I'm designing something, I always use vector masks. When I'm done adjusting my text to my liking, I make that a shape vector mask too (unless the logo is for myself and I know I'm going to have that font, or when I may want to change the font). I design these at the default photoshop size of 5x7 at 72 dpi, because as long as you leave the images in vector format you can certainly resize bigger without any problems to speak of, and as long as the logo is simple resizing smaller is not usually a problem either.
Never flatten the image.. to be safe I always just select all, copy merged, and then save that at filename-merged.png or whatever. You can make a flattened image smaller with a wee bit o sharpening, but if you try to go bigger it'll look bad.