What are the best BES12 Custom apps not using the proxy?

My knowledge on BES12 is limited as I only do the app development. The problem is this

When using the secure workspace to access the corporate network we have some applications that need to access through the proxy. These are custom applications on ANDROID devices

There is a PAC file defined which the phones/tablet browser uses, but no way that I can see to make applications use this proxy.

Is there some kind of settings on BES12 admin or within the application itself that has to be enabled to allow an ANDROID app installed in the secure workspace access through the PROXY

Thanks