You can use LayoutStyle property of ToolStrip. You need to set up it to Table and modify layout settings (specify rows and columns count).
You can do it like this:
this.toolStrip1.LayoutStyle = ToolStripLayoutStyle.Table;
var layoutSettings = (this.toolStrip1.LayoutSettings as TableLayoutSettings);
layoutSettings.ColumnCount = 3;
layoutSettings.RowCount = 3;
And the you can add new items to toolstrip:
var item = new ToolStripMenuItem(string.Format("item{0}", this.toolStrip1.Items.Count + 1));
this.toolStrip1.Items.Add(item);