Before you start retuning Flexi-Capo "fingered" strings first check the finger covering any out-of-tune note by making sure it is seated properly on the string and then try tweaking the note with the finger itself, rotating it more or less to sharpen or flatten the note as required (i.e. adding or reducing the pressure on the string). More often than not you will be able to tune notes perfectly without having to resort to using your guitar tuners at all. 

When you first start playing acoustic guitar you may find it hard to get a good sound from it, especially if you are a beginner with soft fingertips. The notes you play will often sound dull and rather stilted and the music doesn't flow nicely. So think about the sound you are creating as you play, try to make at least some of the longer notes sound "sweet", using your fretting finger to add a vibrato effect to the sound. Classical guitarists typically do this by moving their fretting fingers back and forth along the length of the strings whereas blues, rock and electric guitar players tend to bend them by moving them from side to side. It helps if you have access to a recording device of some kind so you can frequently record and listen to yourself playing as you develop the technique. Becoming emotionally involved in the music you play will have a profound effect on your desire to create the variety and quality of sounds which the guitar is so capable of producing. So don't hold back!