@ianandrews292: What exactly are you having problems with? Some things to keep in mind:
(Missing) glyphs are per console/site. That means the site in the north (where you meet a certain P....) has it's own set, the site in the west has it's own set, and the site in the southeast has its own set.
You only need more glyphs if you still have '?' symbols on the decryption console. If you don't, you can try solving the puzzle.
Keep in mind: You need to solve the north site first, the other consoles won't work until you do - you can collect glyphs, but the consoles are inoperable at first.
Typically (at least on the 'starter' puzzles) the following works: Aim the scanner at the console and follow the cables - they each lead to a glyph. Glyphs are typically on top of or behind things. If you can't get there, there are some pillars around you can raise up with a separate console (southeast & west sites have this). Just use the scanner, follow the blue line, use the attached console, then you can jump where you need to go. (Later consoles, especially optional 'bonus' ones might not have cable hints - you will really have to look everwhere)
Get comfortable with the mechanic of using the scanner to see what leads where - you're gonna use this a lot.
On to the puzzles: If there are no '?' symbols, just do what it says - fill in the board so there are no repetitions per row, column or outlined subshape. Just click each 'empty' spot until it has a fitting symbol. If there's a 4 symbol row/column/shape with three symbols filled in, start there. Move on from there....
Later things get kinda trickier, but the 'learning curve' is okay.
@Sludge-Gulper: Try 'easy' and a somewhat more tactical approach maybe? You'll need to learn to deal with those pesky remnants - otherwise you'll have