You have to have plan what you trying to do, shape itself is not as big problem as it may look. But you have to have plan. I used 2 defenders and 1 HB only as defensive players, but I was heavily marking and pressing opponent and it worked. I placed my players close to his players and marked them to deny them space, so my back two were enough as I was dominating possession and playing mostly on opponents half. This had its own risks, and I understood them, but this is something that you need to understand too.
When you are playing with only two CB-s and only two wide players, you can not give them permission to dribble, as there is no one who can cover them without leaving you wide open, and you did exactly that by giving them attack mentality. You want them to use space without ball, not to dribble at defenses, loose ball and live you open. Second issue is that with your extreme offensive mentality and three strikers, you have very few players that are defending even when your defense is set. You may want to use at least two of them to mark opposition players, in order to help out while defending, as your front three will be bypassed very quickly. And third issue is that you leave a lot of space between defense and midfield trio, which can be exploited, and you have to recognize when this is happening and react by moving one of your 3 MC-s to DMC position. Finally, you have to be very careful with your WB-s so they would not leave their position and leave holes due to much more pressing shout. You have to keep them in place as they are only ones who are defending wide and they have to play much safer game. And finally, try to play little slower, control game more, to be more in control of what is going on, and not loosing too much balls due to extreme tempo of yours.
Your second formation is bit like this one,
Lobanovskyi's Mythical Tactics for FM14
But you notice the difference, and notice what this gay wanted to achieve with each shout, and see how it is different from your approach, you may see why.
I am guessing you were trying to do something like this:
Emulating Diego Simeone's Atletico Madrid
I have not tested it, so it may work, but I see some issues similar to your approach.
To understand better what is all about in this formation and this approach, read this, you may get some ideas:
A Guide to Atletico Madrid's Tactics Under Diego Simeone
Your issue is that due to flexible shape, your defensive shape is crashing down, and you leave space with this aggressive closing down, and second issue is that your players are too far apart to be effective when pressing. You need to think about these issues and to understand how you can get better results.
I had used similar formation and similar view with success, but it was more of attacking/control mentality, and it was very fluid. Reason for this is that you want to bi extremely aggressive when in transition, and the way to achieve this is give everybody permission to join counters when opportunity arises. Second, you want your team to cover each other and do not leave holes in your defensive shape while closing down. And finally, You have to play a bit with your width, sometimes, it could be useful to play bit wider, sometimes it is good to play narrow. Just watch game and see which are the problematic areas, and how you can plug them by using your width.
One more thing, with this mentality, you may want to use defensive forwards, as they are quite useful while defending, and they are great at giving you time to push up the field in counter attack.