@WiZaxx
Let me see if I can explain in < 1000 words… 🙂
The X, Y properties are top-left coordinate of the selected component relative to its container.
The Resize Properties control represents the layout constraints of the selected component (center rectangle) relative to its container. So the red bars represent the left, top, right, bottom margins of the container to the component. A strict margin is set when the red bar is highlighted. Unfortunately the properties does not yet show the actually margin value (coming soon). If a margin is not set then a proportional margin in percentage is set.
For me a picture + a design file is worth 10,000 words. Would you mind sharing your design file with me to inspect the alignment issues further. You can send it to support at genuitec dot com with subject “MobiOne file for wayne from WiZaxx”. I’ll give it a look asap.