In TradeStation, indicators can be placed on top of a chart or in their own sub-graph. A sub-graph is an area below the price chart that's aligned with the price chart. TradeStation allows you to put more than one indicator on a sub-graph, just as you would on the main price chart.
If you have more than one indicator on a sub-graph, and that's not what was intended, you can move your indicator to its own subgraph. One way to fix this is to use Format/Analysis Techniques, select the indicator that you want to move to a separate sub-graph, and choose Format, then select a new sub-graph for the indicator using the Scaling tab. You can select subpanel 16 if you just want to make sure it's at the bottom. Select the other indicators that may be sharing the same sub-graph and put them on their own sub-graph as well, and the problem should be resolved. You can use this technique to rearrange the order of indicators on sub-graphs.
Note that you can also rearrange the order of indicators by left-clicking on them, then dragging them to a new position. You can let go of the mouse button where you want it to drop, though you want to be careful not to drop one indicator on top of another. The cursor will change to an asterisk-like cursor when you're between two sub-graphs if you want to position the dragged indicator between two other sub-graphs.