Hi Kerushan

Thanks for reaching out on Lucidchart community! Unfortunately there is no in built way to limit the auto layout to stay within the margins. Currently you will need to use auto-layout then adjust your objects within the margins. If you are using the Grid option in Auto-Layout it usually does not shift them very far just aligning them to a grid. If you are using Hierarchy you can order them that way then move them to where you would like them to be within the margins and use Grid to make sure they are properly aligned with relation to each other. 

Would you mind adding your idea for margin bounds to our feature request form? These ideas are sent directly to our development team for their consideration.

Thanks!