The cause of all negative emotion is resistance.

What happens when you meditate? You distract yourself from your thoughts, you stop your thoughts. And when there are no thoughts in your mind, there can't be any resistance to any thought either.

So your vibration automatically raises to a place of love, which is your most natural and pure state. Consequently you feel good. It's like when you hold a cork (your thoughts) under water. If you let go of holding to it, the cork raises to the surface automatically.

But if you have thoughts (guilt) that are too intense so they don't let you stop your thinking, you better deal with them first before you go on. Or they will persist even more. Remember

What you resist persists.

So here is what to do:

1. Look at that guilt feeling. Let it be. Welcome it like a good friend that you haven't seen for a long time. Say hello and let it be.
2. Embrace the guilt feeling and it's manifestation in your body. There will be some sensations, probably in your chest and stomach area (or in other areas).
3. Observe those guilt sensations in your body and talk to them. Really do this. "Guilt sensation i am here with you. I know you are here to help me. I am here to listen to you. I will give you my full undivided attention."
4. Describe the characteristics of these sensations. What size to they have? Do they have a specific shape? Do they move or do they stand still? Does it feel like pressure or more like tingling? Which shape does the guilt sensation have? Describe as much (physical, not emotional) characteristic as you can.
5. Oberserve neutrally and stay with it for a few minutes. If you loose your focus, go back to 3.

You will notice that this guilt feeling (or whatever feeling) disappears if you are willing to listen and don't run away as if this sensation would kill you. Afterwars you can go on with your meditation session smoothly :).

This trick helps me every time, no exeptions! It's the most powerful meditation form to deal with emotions and neutralize them.

@releaser99 has more or less sown in all up in his excellent answer but I will just add this.

You mention how you have to motivate yourself to meditate. Depression will most certainly play a part in that, but it might also be because you have the thought of having to sit and meditate for longer periods to get the benefits. I have found this not to be true at all. You don't have to meditate for very long at all to get the benefits.

Here is an short meditation exercise by Dr Frank Kinslow you can do here and there throughout your day and only takes a few minutes.

Thought Stopping Exercise by Frank Kinslow

See also One-Moment Meditation

when you meditate you calm the water and make them pure so you can look at the light in the water that light is you the though and emotion that you see they are yours. and there is lots of stuff still in duality and not solved or ignored. until you solve it by learning all the truth about it it will come back again and again. so continue the meditation solve the puzzle. see how it all relates together learn the truth and be set free.