Running a Webinspect scan on the E1 and E2 environment of an application simultaneously. Thoughs Please...
WebInspect desktop permits you to run two scans at once, but there would be nothing particularly special about lining up these two scans at the same time. You would want to review your machine's resources (RAM, CPU) against the WebInspect 10.40 requirements (see the Fortify 4.30 System Requirements document at WebInspect 10.40).
You might prefer to run the first scan, then re-use its scan settings for the second one. The scan settings can be extracted at either the end of the Scan Wizard ("Save scan settings"), or when the scan is Completed or at any Paused moment by clicking on the Edit menu > Current Scan Settings > Save As. Once you have the settings, you can edit them from the Edit menu > Manage Scan Settings, or even by loading them in as the Default Scan Settings and re-saving them from that perspective (Save As).
To utilize the saved settings, you can either set them as your new defaults for the next scan (open the Edit menu > Default Scan Settings > Load Settings From), or you can load them directly into the Scan Wizard. This option has slightly different methods depending on the scan wizard used. In the newer Guided Scan Wizard, you can select the desired scan settings when it shows among the "Recent Templates" area of the first screen, or by clicking the Advanced Settings button later (toolbar area) and loading in the saved settings file from there. In the older Basic Scan Wizard, click the pick-list next to the "Default Settings" button shown in the lower left-hand corner, and it will list your current library of saved (XML) settings files.
Once you have your two scans, you can run the Compare feature, which is a visual Venn diagram UI without output options (screen capture it). You could run a Duplicates, Aggregate, Trend, or other relevant reports. Be sure to select both scans in the first screen of the Report Wizard before you get to your report template choices.
Alternate to all of this, you could run one scan that encompasses both Hosts. To do this, you would need to specify one Host in the Starting URL field of the scan wizard, and add the second host specifically to your Allowed Hosts scan setting. Depending on the link paths, you might want to manually add a page or two from Host2 via the scan wizard's choices or a Start Macro, just to ensure the scanner is able to locate further links.