Richard,
The setup you describe is correct.   As long as you have the interface 
cable plugged into the  back of the radio, the internal tuner is 
disabled on ant 1.

On another note, the amp will do 6 meters, but the998 tuner won't.  I 
don't know how much 6 meter stuff you do, but if you want to run the amp 
on 6 (assuming your antenna can handle it) you may have to juggle some 
things.

73, Steve KW3A

On 1/4/2016 6:41 PM, Richard B. McDonald wrote:
> Hi!
>
>
>
> Below under the "***" are copied the relevant sections of the TS-2000's
> manual.  Essentially, I have an external MFJ-998 auto tuner connected to an
> amplifier (Ameritron ALS-1306), which then connects to  ANT1.  On ANT2, I
> have a 6M J-pole, which does not run through the amplifier.  Is my
> understanding of the below correct that1) if I am on ANT1 pressing the AT
> button on the TS-2000 engages the MFJ-998 auto tuner relative to the antenna
> connected to ANT1, and 2) if I am on ANT2 pressing the AT button engages the
> TS-2000's internal antenna tuner relative to whatever antenna is connected
> to ANT2 (my 6M J-pole?
>
>
>
> 73,
>
> Richard KK6MRH/AG
>
>
>
> *  * *
>
>
>
> Page 72 - [INTERNAL] AUTOMATIC ANTENNA TUNER: 2.Press [FUNC], [AT/ANT1/2] to
> select ANT 1 or ANT 2. If an external tuner is connected to the ANT 1
> connector, select ANT 2 to use the internal antenna tuner. The internal
> antenna tuner is automatically bypassed if an external antenna tuner is
> connected to ANT 1.
>
>
>
> Page 94 - [EXTERNAL] ANTENNA TUNER: Use the ANT 1 and AT [auto tuner control
> connection] connectors to connect an external antenna tuner. If you connect
> the external tuner to the ANT 2 connector, the external tuner will not
> function [by using the rig's tuner control, AT button].
>
>
>
>
>