The following is quoted from this website: http://www.skysdaughter.com/icom746-faq/
Q:3.2.6 Can I use the internal ATU along with an external ATU?
Maybe. Theory says yes, but Icom says no. The results
are mixed. Use at your own risk.
Many people use an external ATU along with their IC-746.
Usually, they leave the external ATU switched to "bypass"
and let the internal ATU do its thing. For troublesome
bands/antennas, they turn off the internal ATU and
engage the external one.
Others use an external ATU to match their antenna to
the middle of the desired band and let the internal ATU
handle the rest. In theory, the ATU doesn't know or
care what's hooked up to it; it simply tries to match
up to the impedance it sees.
In most cases, either of the above approaches work fine.
Many hams have been applying both for years with no
However, some IC-746's have had their ATUs go out from
fried detector diodes and driver transistors. On many
repairs, Icom has blamed the failure upon external
tuners. One ham was told that external tuners can
cause problems even when they are switched to "bypass".
Nobody has been able to adequately explain why an
external tuner would cause such damage, particularly
when bypassed. Some speculate that tuning with low
power is safer than tuning with high power (if nothing
else, its at least more polite).
We need more information on this, but at least you've
The best procedure we can suggest at this point is:
* Turn off the internal ATU.
* Reduce power to about 1/4 (25w).
* Adjust the external ATU using the rig's SWR meter.
(The two meters usually disagree. It is what the
rig sees that is important.)
* Restore full power.
* Turn on the internal ATU.
Do not adjust the external ATU at full power.
Do not adjust the external ATU while the ATU is on.
Do not change frequency while the ATU is searching for
Now some agree with this and some do not. In laymans term, the interaction between the components with high voltages present could possible damage the smaller/lesser components of the internal tuner. It's up to you to make your own decision.
I do not think it's worth taking the chance.....I have seen too many fried internal tuners.