1. I would recommend going with PSZ and using the Detailed Edit mode in eQUEST to create a system for every zone. If this is cumbersome, you could also go back to the eQUEST wizard mode and create a PSZ system and assign it to every zone. In the HVAC System Wizard, this is done by choosing System Type: Packaged Single Zone DX and System per Area: System per Zone. The PSZ system type is more flexible than the PTAC system type and allows you to use a wider range of options for heating and cooling. It is also the system type used in the Daikin VRF Guide.
2. This sounds very odd. One would expect the heating energy to be lower with a heat pump (which typically uses electric heat as a backup when the heat pump can't provide enough heat). I just tried creating a model in the wizard, and switched the heating type from heat pump to electric for a PTAC and the heating energy went up as expected. Can you provide any more information about your model? What is the climate zone? Do you have unmet heating hours? What is the Heating Electric Input Ratio for your heat pumps?

1. Always use the system recommended by the manufacturer of your VRV. eQuest can't model VRV properly, so manufacturers choose a given eQuest system and create custom curves for THIS system in order to approximate what's going on. That's why they give you a modeling guide and eQuest curves, so use that. It will also help you justify your approach if you're doing this for compliance or an incentive program.

2. As far as heating going up with heat pump compared to elec, it's likely a modeling mistake and/or lack of analysis of the model's output (unmet hours in particular, maybe outdoor air as well). @Daniel's suggestions are on point and also where I would start to debug.

@crduggin just refreshed my memory. As of July 2014, there was still a mistake in Daikin's curves: eQuest has a limit of 80 characters per line... If you put more it gets truncated.

I emailed some rep twice about it, I don't know if it was corrected or not.

Here's a message I wrote in July 2014 to the eQuest user mailing list:

I've been trying to model a Daikin VRV system and trying to figure out why I was getting 100 times more space heating in the proposed (VRV) model compared to the baseline model (PTHP). After isolating the problem to the VRV, I found a conversation from March 2014 between a few folks (Byron Burns and Bill Bishop mostly - thank you both!), that basically explained why I was getting the issue: the .inp data from Daikin isn't importing correctly.

I just wanted to say that we're in July now, and this still hasn't been fixed (I downloaded the curve from Daikin a few days ago), so if you're having the problem, the fix proposed by Byron and Bill still works. It consists in to replacing the VRV Heating Curve with:

"VRV Heating EIR-F-EWB/ODB AC" = CURVE-FIT      
    TYPE             = BI-QUADRATIC-T
    INPUT-TYPE       = COEFFICIENTS
    COEFFICIENTS     = ( -1.85025, 0.0620141, -0.000312822, 0.07145853,
        -0.0003626328, -0.0007776424 )
    ..

I have tried to use the Daikin curves and modeling guide, but it yielded the same results. I believe there is an error in the VRV Heating EIR curve because if i set it back to the default PVVT curve, the heating energy is more reasonable.

As per Julien and Daniel's suggestion, if we model VRF system considering one system per zone, then how do we input the cooling capacity and supply CFM for each system. Also how much additional savings can we expect considering Daikin curves (versus default DX curves)?