Network Bridge and LAN shaping

I have a question regarding the implementation of SoftPerfect Bandwidth Manager (BM). We are testing the software in the company for our specific needs and the following is the scenario:
- We have two distant networks (10.50.x.y and 10.60.x.y) and traffic is routed through 2 routers and we hope that BM can be used as a traffic manager when it is installed on the server that is placed between those 2 routers.
- On the server (2008 R2) there are 2 adapters which are connected in Bridged network adapter.
- The Bridged network adapter (created on the OS) is present in the adapter list in BM, the other option is Network Bridging in BM it cannot be saved to create a new Network Bridge adapter.

Although the traffic goes through the server (with BM installed) we cannot shape/control/monitor the traffic with any possible rule that is created just like the BM is not present.

Question:
- Is it possible to use BM for this purpose?
- If it is possible, can you instruct me how it can be done (server with 2 adapters and BM installed)? Is the Bridged network adapter solution for this implementation?

The reason Bandwidth Manager does not have any effect in this configuration is that the Windows Network Bridge forwards traffic at a lower level, before it reaches our network driver. In other words, any pass-through traffic never reaches Bandwidth Manager.

Normally in such cases we recommend turning Windows Bridging off and instead using the built-in bridge implementation. Did you have any problems doing this?