If I understood your question correctly, you want the Least Square Means (LS Means) of each haplotype. Since you have results from the Overall Test and Individual Test, you can get two LS Means estimates for each haplotype. In either case, the LS Means for the haplotype is the sum of the Intercept and the haplotype estimate. The LS Means from the Overall Test is conditional on other haplotypes fitted together in the model and it may change if you change the model (say, remove haplotypes from the model), while the LS Means from the Individual Test is unconditional to other haplotypes because the model has only one haplotype.
First, if you are looking for the mean for your trait (PSS_2013) for each haplotype, then take a look at each section labelled Test for Haplotype Hx where x is the Haplotype number. Within each section there is an item called PSS_2013 Mean. That would be the mean for the trait for that haplotype. Is that what you are looking for? These individual sections for each haplotype are the individual tests for each haplotype as opposed to the whole model fit where all haplotypes are fit together (at the beginning) and the PSS_2013 Mean is the mean for the whole fit, instead of the individual fits.
The Parameter Estimates are the slope of the fit for each haplotype as individual tests or the whole model fit and represent the effect (+ is a positive effect and - is a negative effect) on that trait for each haplotype or when fit together, their effect when considering the other haplotypes.
Does that help explain the output?
I must correct myself when I said LS Means in the previous reply; instead, the values I defined as LS Means are indeed the predicted means for each haplotype.