Yes, you can change ALT2GXB PMA (Vod, Pre-emphasis and Equalizer) settings on one of the instances using Assignment Editor in Quartus® II software. All the channels within that particular instance are affected by that change.
Here is the way to change the PMA settings using the Assignment Editor in Quartus II.
1) Find the ALT2GXB instance in the Project Navigator window.
2) Right-click the instance, choose Locate in the sub-menu and select Locate in Assignment Editor option
The Assignment Editor opens up with instance name selected in the To column. 
3) Assign ALT2GXB parameters to the Assignment Name column and ALT2GXB PMA settings to the Value column.
AL2GXB PMA Assignment Names and Values are provided below.
VOD_CTRL_SETTING: This assignment specifies the Differential Output Voltage (VOD) switching control signal for various differential voltages. Values are [6..0].
PREEMPHASIS_CTRL_1STPOSTTAP_SETTING: This assignment specifies pre-emphasis control signal for the first post tap. Values are [12..0]
PREEMPHASIS_CTRL_PRETAP_SETTING: This assignment specifies whether the pre-emphasis control signal for the necessary pre tap is inverted. Values are [7..0]
PREEMPHASIS_CTRL_PRETAP_INV_SETTING: This assignment specifies whether or not the pre-emphasis control signal setting for the pre-tap must be inverted. Values are "TRUE" and "FALSE".
PREEMPHASIS_CTRL_2NDPOSTTAP_SETTING: This assignment specifies pre-emphasis control signal for the second post tap. Values are [7..0]
PREEMPHASIS_CTRL_2NDPOSTTAP_INV_SETTING: This assignment specifies whether or not the pre-emphasis control signal setting for the second post-tap must be inverted. Values are "TRUE" and "FALSE".
EQUALIZER_DCGAIN_SETTING: This assignment specifies the equalizer gain setting. Values are [3..0].
EQUALIZER_CTRL_[]_SETTING: Parameter [A,B,C,D,V]. This assignment specifies the corresponding equalizer control setting. Values are [7..0].
All the channels in this instance are modified by this method. For example, if you have a design with 2 channels per instance then both channels will change. Here is the assignment editor for two channel instance with 2 instances changing VOD and 1st post tap pre-emphasis.
To verify the compilation, go to the GXB transmitter channel settings in the fitter section of the compilation report. Below is the output for the above assignment.
If the To assignment is incorrect in any way, then the above settings will match what was entered into the Mega-wizard since these parameters were not changed.
If your setting value is not legal, it results in a Quartus II Fitter error.
Refer to Stratix® II GX Handbook, Chapter 4, DC and Switching Characteristics (PDF) on the supported values of Vod and Pre-emphasis settings.