I have always wanted to learn how to play guitar, especially Electric. I had a birthday recently and my wife bought me a super cheap setup from eBay. I know there are a lot of reasons to use a more expensive guitar but I think she wanted to see how committed I am before spending a lot. It’s a Stratocaster style and I am having trouble getting it in tune (using the fender tune app). The saddle adjustment screws are not aligned at all and I am wondering if that is contributing to the problem. Basically I am a complete newbie and need some guidance on getting this into a playable state.
There are many useful YouTube videos about setting up a guitar, but here are the basics:
Checking neck relief
Press each string down on the first fret, and press the other side of the string down on the highest fret with your other hand, and then look at the height of the string above the frets around the octave; if the string touches the frets, or if the string is more than a millimeter above the frets, take the guitar to a guitar shop to have the truss rod adjusted.
Play each string at each fret, and listen whether each note rings out fully without the string buzzing against the higher frets and stopping the sound. Raise or lower the saddle with the two screws it stands on, to the lowest settings that has no problematic fret buzz. If you can't find a setting that works, take the guitar to a guitar shop to have the frets checked out.
Tune each string with a precise tuner (a smartphone app may not be sufficient; try the tuner in the free version of the Guitar Rig Pro software, or buy a clip-on tuner with strobe function). Then check a few notes higher up the neck; if they are sharp, move the saddle closer to the bridge; if they are flat, move the saddle closer to the pick-ups. (Loosen the string before moving the saddle, and tune again after.) Be aware that the intonation can never be absolutely precise for every fret along the neck; it's always a compromise.
A smartphone app may be sufficient for tuning once the intonation has been set correctly, but a clip-on tuner will be faster, more precise and more practical. Always tune starting from a slightly flat setting, give the string a good pull or play a large bend, then tighten the string until it's in tune; if you go too high, set it flat and start again.
If while tuning you notice that you can turn the heads without the pitch changing, and then suddenly it jumps up (sometimes accompanied by a ping sound), the strings aren't moving freely through the nut slots and/or the string retainers. Adding graphite from a pencil may help, but if the problem persists, take the guitar to a guitar shop and have them file the nut slots for the string gauge you're using.
New strings may take a while to 'set'. After you've changed the strings, put them roughly in tune, then pull them away from the fret board repeatedly at different points. It may be necessary to tune them up a turn or two and leave them like that overnight, until they are sufficiently stretched, and their tuning stabilizes. (Be careful not to break strings near your face!)
The saddle adjustment screws are supposed to be different, and it looks like what you have for saddle positions is not unusual.
If you can edit your question to include more details about what kinds of tuning problems you're having, we can give more detailed answers.
I will note that learning to tune effectively is part of learning to play, and you should practice tuning every day and expect that over time you'll get better at it. And it's normal to start off having some trouble tuning.