Update:
After discussing this with Bottomline Tecnologies staff and having received some .pcf_ps files, here is my understanding on how create!form works and what needs to be done to resolve my original problem. If there are any corrections to this information please let me know.
Create!form processing by passes the printer drivers and send postcript directly to the printer. Thus the printer properties settings such as input tray and orientation are ignored. However settings that are on the physical printer itself are used.
The Lexmark T654 uses different code, in certain cirumstances, to that produced from Create!form. The printer tray falls into these circumstances. Thus, regardless of the printer tray specified in the design of the Create!form project, the default tray, as defined on the physical printer, is the tray that will be used.
To get around this Create!form has a tray mapping facility. This creates a file with the printer driver name as the filename and a .pcf_ps extension. For print queues defined in Create!form Server 6 (as opposed to Server 3), which is where the ARD printqueues and projects are defined, this file needs to be in the following directory:
C:\Program Files\Create!form\SystemResource\Device
Any printqueue that uses the same driver will use the same mapping file.
However the Lexmark T654 PS3.pcf_ps is created without any mapping and the mapping code has to be inserted.
When a tray is specified in the design of the Create!form project, other than default, the tray mapping file is inserted in the code sent to the printer. If the default tray is specified in the design of the Create!form project the tray mapping file is ignored.
Using the Create!form Server 6 printqueue properties, a different mapping file can be specified and therefore will not use the mapping file with the same name as the printqueue's driver. However if the default tray is specified in the design of the Create!form project this tray mapping file is ignored too.
To specify a different tray mapping file, open the printqueue properties from with Create!form Server 6. In the General Properties there is the option to specify a default merge configuration. By clicking the down arrow and selecting Manage, configurations can be created, changed and deleted. When creating or editing the merge configuration, in the postscript properties, there is the option to use a printer control file. This is the tray mapping file. The drop down list will contain all files in the C:\Program Files\Create!form\SystemResource\Device directory with the .cpf_ps extension.
Now, taking into condsideration the above, here is how, I believe, things need to be set up to allow tray 2 to be used:
1) create a printer control file (aka tray mapping file) that maps tray 1 to tray 2 using the appropriate code. Do not name this file with the name of the printqueue driver.
2) edit the Create!form Server 6 properties of the printqueue concerned and assign a merge configuration that uses the printer control file in step 1.
3) edit the Create!form 6 project concerned and make sure that it specifies tray 1.
Now when a print job that uses a Create!form 6 project that specifies tray 1 is printed on the printqueue, it will print using tray 2.
If there is a need to print a print job that uses a Create!form 6 project that specifies tray 1 on the same printer, I believe this is what needs to be done: create a different Create!form Server 6 printqueue that points to the same printer, ensure that it will not use a printer control file, it will print using physical printer's default tray - usually tray 1. If there is a need to override the physical printer's default tray, then create a printer control file that maps tray 1 to tray 1 using the appropriate code and set up the Create!form Server 6 printqueue to use it.