Hi Vikas,
In newer versions of SBO (since 9.0 I think but the functionality might be in 8.8x) it's been possible to manage form settings for multiple matrices or grids on the same form via code. The UI API Form object has a Settings property. This has a MatrixUID property which you can set to the uid of the matrix that you want to control via the Form Settings window. Only one matrix can be set at a time but you can swap between them using code. There's a sample in the SDK which is number 21 in the COM UI section.
Kind Regards,
Owen