If you ran the HT pre out into your tube pre, you'd probably have to crank the volume high on the receiver to get sufficient volume from your tube preamplifier. But the way you had it, you were still going through the HT receiver's internal processing, which is less than great.
If you have direct, multi-channel (6- to 8-channel) inputs on your receiver, you can hook stereo analog sources into your tube preamp. Then run the main tube pre outputs into the left and right main direct multi-channel inputs on the receiver. You don't need to use all the channels. That configuration worked very well in my system and it avoids putting the signal through the receiver's internal processor. You'll have to experiment with where to set the preamp volume to get good output through the receiver volume. Then, you can either use the amps built into the receiver or take the L and R preamp outputs from the receiver and run them into your stereo amp. That setup should work fine.
My 6-channel inputs run through the volume control on my receiver but some receivers may bypass the volume control in the direct mode (usually not), but start with the volume set low on the tube preamp until you know if you are going through your receiver's volume control or not.
And you can still run a digital output from your CD player into the HT receiver (analog too, if you want), or run your analog CD/DVD outputs- through the tube pre.