I did some pandaboard kernel development back when and found the makefiles are best structured for a first-time build, which is great but means they are slow for build cycles.
Yes "make bootimage-nodeps" is a clean way to make just "boot.img". I have a couple additional thoughts. I don't have a running pandaboard at the moment so this is taken from my old build scripts. And I used the linaro baselines, which are different from the AOSP (e.g. uboot instead of the Android bootloader). So you will need to massage these thoughts some for your testbed.
I use $(PRODUCT_OUT) as a short-cut for the shell functions in envsetup.sh, $(get_abs_build_var PRODUCT_OUT)
1. backup the current $(PRODUCT_OUT)/kernel so you can recover a working kernel if something goes bad
2. copy the new kernel zImage to $(PRODUCT_OUT)/kernel
3. make bootimage-nodeps creates a $(PRODUCT_OUT)/boot.img containing your kernel. MUCH faster is to use the umkbootimg, boot_info, mkbootimg utilities (google for downloads) to update boot.img.
4. Load JUST the boot.img onto the pandaboard. system.img requires all the vendor proprietary shared objects, which I found to be tedious/slow for kernel work. Use "fastboot boot $(PRODUCT_OUT)/boot.img" on a running system to boot your image but NOT overwrite internal flash. If you are putting it on an SDcard use dd to overwrite the by-name LNX partition. This is generally the first partition on the sdcard.
Good luck!