To get the kernel seen in the menu list, now you need to edit your ubiboot.conf (which in default is in your /home/user/MyDocs/boot/ directory...)

1.) find the place where it says # Harmattan kernels
for example, in my device it looks like this:

# Harmattan kernels
G_HARMATTAN_NUM=5
G_HARMATTAN_AUTOBOOT=0
G_HARMATTAN_1_LABEL="2.6.32.54 + fbconsole"
G_HARMATTAN_1_FILE="/boot/Harmattan/boot/Image-2.6.32.54-fbconsole"
G_HARMATTAN_2_LABEL="2.6.32.54 Nemo backport"
G_HARMATTAN_2_FILE="/boot/Harmattan/boot/zImage-2.6.32.54-juice_backport"
G_HARMATTAN_3_LABEL="Nitdroid pr13 kernel"
G_HARMATTAN_3_FILE="/boot/Harmattan/boot/zImage.pr13"
G_HARMATTAN_4_LABEL="Openmode + L2fix"
G_HARMATTAN_4_FILE="/boot/Harmattan/boot/zImage_2.6.32.54-openmode_l2fix"
G_HARMATTAN_5_LABEL="2.6.32.59 kernel+xxx"
G_HARMATTAN_5_FILE="/boot/Harmattan/boot/zImage_2.6.32.59-plus_nat_extfat-20121301"
G_HARMATTAN_6_LABEL=""
G_HARMATTAN_6FILE=""

2.) The tag G_HARMATTAN_NUM=5 means that the kernel menu holds 5 entries. (5 kernel name lines are shown)
You need to put here a number from 1 to 6, depending on how many kernels you have.

3.) The tag G_HARMATTAN_AUTOBOOT=0 means that there is no autoboot active now. If you change that to number 1...6, then when you press the Harmattan icon, that kernel number will boot automatically, it will not ask for which kernel to boot.
This is useful, for example if you have just one kernel under an OS, for example Nitdroid and always want to boot it.

4.) Each of the tag pairs, G_HARMATTAN_x_LABEL and G_HARMATTAN_x_FILE signify one kernel menu line.
For example, I have G_HARMATTAN_1_LABEL="2.6.32.54 + fbconsole" which means that this text is shown in the menu as the first kernel line.
When I press that line, ubiboot will search for the file specified by the corresponding tag G_HARMATTAN_1_FILE="/boot/Harmattan/boot/Image-2.6.32.54-fbconsole"

So, now you know how this is constructed. If you want to have this kernel you downloaded as the first line, you will need to set the tag G_HARMATTAN_1_LABEL to some name for it (anything is OK, it's yours to decide) and the tag G_HARMATTAN_1_FILE as your kernel path, "/boot/Harmattan/boot/zImage_original_PR13_nokiasigned" for example.

(note here that the file path is /boot/zImage_original_PR13_nokiasigned when you are looking at it in Harmattan, but when you are running ubiboot the device has very different root file system, and then the file appears as /boot/Harmattan/boot/zImage_original_PR13_nokiasigned. This can be confusing for some people...)