I am having trouble knowing exactly what to practice in order to make consistent progress. So far, i will just play bits of songs that I know and maybe do a few scales, but there is no order to what I play...

My goal is to be able to be able to improvise and put sounds together on the spot. So I feel like I need to become very familiar with scales and different keys? But I have no idea how to learn it.

Any advice?
1. Learn songs. Try to learn how to play some songs that you know and which inspired you to take up the instrument
2. Try new techniques. Learn to implement things that inspire you to become a better player. A good place to start is power chords and the pentatonic scale
3. Don't underestimate the power of noodling. Put on a backing track, and just kinda go with it. The power of improvisation shouldn't be underestimated
4. Practice EVERY DAY. This should go without saying, but try to pick up a guitar every single day without breaks. Even if you practice as little as 30 minutes some days make sure to get practice every day.
Make a list...create a road map of where it is you want to be, both long term and short term.

I can't stress enough, the importance of having a plan...you're just starting out and are already seeing what will happen if you just take the approach of taking stabs in the dark to learn. This applies to anything.

Like Drew said, take inspiration from what inspires you (duh)...dissect what techniques are implemented in what you want to play and go from there.

Do you just wanna have fun and be able to play popular songs? Learn the open and barre chords, THEN concentrate on the other scales. Get rhythm down before solo stuff.

Want to play lead? Get those scales and patterns down...maybe work out a few of your fav. licks. Keep it clean.

Also, +1 on the noodling...I always screw around a little when warming up or after a good session of practice. It keeps things fun when you're done doing nothing but sweep patterns over and over for an hour.
Watch great players play and get inspired. If they can do it, you can too.
Another thing I didn't think of at the time that applies to aspiring lead players...

I was taught, from vids and a teacher, that the best way to get separation in your fingers for the purposes of building speed, was to do random chromatic Petrucci-like patterns as fast as I comfortably can.

I did that for years and it is beneficial...but if I were teaching someone that same theory...I'd say to use exotic scales instead. Not only are you learning what was intended...you're also learning the scale patterns, instead of just patterns...AND learning something that will add flavor to your playing.

Things like the Japanese Scale and the Byzantine Scale will have you moving across strings in awkward patterns that you aren't used to...tackling the tight Blues Scale seems like a joke after stretching out for eastern scales at speed.
Only problem is, most people are inspired to play guitar by hearing and watching brilliant guitarists, and immediately want to be able to playthe same things, which are obviously way out of reach. Learning basic open chords and barr chords will help get the fingers to go where you need them to and build strength. Learning to switch between chords, and to go from a strumming pattern to playing single note stuff and scales so that from the beginning you don't get too locked in to just either one.
Find a song you know and love that seems as basic as you can, and just try to learn little bits of it at a time, don't try to run before you can walk, the worst thing is teaching your fingers to play badly things that are too complicated at first. Much better to play something simple as cleanly as you possibly can.
Hope some of that is of help to you!
Here's a method for you. Figure out how much time you are about to devote to playing guitar. Let's say you have a half hour. Break up that half hour to make it the most productive. Here's an example:

5 Minutes: Warm Up
5 Minutes: Scale Drills with Metronome
5 Minutes: Practice Sweep Picking
15 Minutes: The song you want to learn or play to a jam track.

I always found that if I broke up my time into segments, that I would get the most accomplished. It definitely helped me out. Hope it helps you.