Let me try to rephrase what I was trying to say.
First, LFE (Low Frequency Effects) is a separate channel in an input audio file. On input, it's the .1 of a 5.1 audio track, for example. In other words, on input, the .1 channel = LFE audio channel. Music audio tracks usually don't have a .1 channel, but movies usually do (for explosions and the like). The LFE channel is allowed to contain frequencies up to 120 Hz.
For output to speakers, people often use the 5.1 notation, too, but it means something different: the .1 stands for the subwoofer output speaker channel. The subwoofer normally receives the sound from any LFE audio channel plus the low frequencies which originally were in the other input channels, too. That redirection of the low frequencies to the subwoofer is called "bass management". Usually, frequencies below about 80 Hz are redirected to the subwoofer. 80Hz is called the "crossover frequency". Depending on the type of speakers you have, the best crossover frequency might be different: below 60Hz if you have large speakers or higher than 100 Hz if you have small speakers.
Two channel lossless WMA audio files don't contain that separate .1 LFE input channel. Their audio is described as 2.0: 1 right front audio channel + 1 left front audio channel with 0 LFE. The front two channels do contain low frequencies, but there's not a separate special effects channel.
You have several bass management options:
1. You can enable "enhancements" in your computer and have it do the bass management
2. You can enable bass management in your receiver so that it is the device which redirects the lowest frequencies of the left and right front audio channels to your subwoofer. (Most front speakers, even the best floor standing speakers, really can't reproduce the lowest frequencies very well. A subwoofer can: that's what it is designed to do.)
3. You can use no bass management at all, perhaps losing the lowest frequencies of the audio track.
You originally were asking about doing bass management in the receiver. Remember, that really is separate from LFE.
To enable bass management in a Yamaha receiver you need to use the Speaker Setup menu. Select Config. Verify that the Subwoofer is set to "Yes". Then make sure all of your other speakers are set to "Small". That really means "enable bass management". It is not a description of the physical size of the speakers. It's the default, but your description of the sound you're getting suggests that someone changed them to "Large" which is inappropriate. Then choose the Crossover Freq. 80 is a good place to start and is the default. These are the most important settings. Refer to your receiver's manual for a description of the others.
I hope this helps a little.
Marantz SR7009/7.1.4/FH+TM/DefTech PM1000/LCR+TM amped