As you have mentioned , I can try changing setting in 'installer mode', but before that how will I feed port 3 in ST9400C and should I still discard port 8 in ST699
EDIT:
Having looked at the ST9400c instructions, if part gravity / part pumped is the type of system you have. It appears that it may be possible to configure the ST9400c as a Mini-Programmer to make it suitable by changing the Installer Parameters to select it. However, the wring will need to be changed so the function of each of the cables you have will need to be identified. Here's the comment from the ST9400c instructions:
"3. It is recommended that gravity circulation hot water systems are fitted with a suitable hot water control valve as shown in the Sundial C-Plan system. For systems installed without this valve, ST9400can be configured as a Mini-Programmer. This is done within the Installer Mode (see page 3 for details). Refer to Honeywell for details of suitable wiring schematics."