How can I subtract a component from a new model

I am a simple maker that is trying to create models to use in my home. I am working on a bottle holder for my guinea pigs and am currently stuck. I have created a model for the bottle and am now trying to subtract it from the main bottle holder. 

I am using the xDesign online tool to create this. 

My bottleThe holder + bottle

I have inserted the model using the "import" tool. This is what it looks like in the Design Manager: 
 

 

When trying to use the subtract feature I get the following error: 
 

If I try to place the object as a geometry that makes it locked into place.

 

What would be the proper way to handle this? 

 

Thanks!