Will upgrading my amp for el34s to kt90s help?

It should. EL34's are not known for their strong, very present bass or low end grunt at all. They are a midrange and treble tube mostly, that is why so many guitar players use them. A bass player, if using a tubed amp, would use KT88's or 6550's in most cases. Those tubes are designed for higher current draw and have inherently stronger and more dynamic bass (presence of it and punchiness). KT90's are variants of the KT88's and should be a good improvement.

I agree on the Magnum. I have the Rogue Cronus Magnum as of about one month ago. I'm actually having the opposite problem you're having. I have a little too much bass. Prior to this I had Rotel separates and I had almost NO bass. The difference the Cronus Magnum made was more than significant. Rogue is a fantastic company. You should call and speak to Mark O'Brien.

The Atlas in Magnum mode is far better than the stock model and for only $600 more the power supply is substantially bettered as well as resisters .the EH kt-90
tubes are excellent now the amp has balls and finesse .
I like the sound of this even better than the stereo90
which is $500 more, also the caps are Mundorfs which are excellent German caps and bypassed with a 1% tolerence caps and the transformers are of super high quality ,Please remember you have 8 and 4 ohm taps take off the cover and try this for impedance mismatches of speakers make a world of difference especially on a tube amp ,also with the Atlas each tube is individually biased
and it is a snap with the excellent meter in the middle
meaning if a tube goes you no longer have to buy a pair.
For $1800 The Rogue Atlas Magnum is far better built and sounding than any competition at this price and looks way retro cool doing it .There is no overseas amp that is built this well, looks this good with sound to match
at anywhere near this price ,The Magnum is the way to go !!

I have polk tsi400 speakers (insert laughter). They can accept biwiring, I'm not sure that I can run the integrated at the same time that it is functioning as a preamp. I will give it a shot and tahnks again. Let me know if you have any other suggestions. The atlas upgrade costs $600 with the new KT90s. I don't mind spending the money if it assures me an increase in bass!

I saw the price for that deal which is near 1.4k for 1 hour effort. I would go to DIY recipes and find it rather simple and save big$$$.

I have heard the Cronus integrated both regular and Magnum,the Magnum upgrade did wonders for the sound in all areas.The Atlas is the power amp section of the Cronus so similar results should be heard.Try to listen to an upgraded Atlas if at all possible.

What speakers are you using?
It might work for you if you connect your integrated and your Rogue in biamplification through the active crossover with better cost efficiency vs. upgrading to KT90.
You can also consider to get tube model with larger power once again vs. money you've allocated for this upgrade.