My levels are connected. I use the lower level to run passenger and freight trains with the upper level as the Beer Line. The upper level is, in essence a switching layout where I shuttle reefers between the upper and lower levels and among the brewery buildings. The climb up is rather steep, which limits the number of reefers to four (plus a transfer caboose). The whole layout is 8 x 23 with the upper level at 8 x 16. The attached crummy picture shows the turnout leading up to the Beer Line. I treat the upper level as a separate block. I'm very happy with this configuration because it gives me the best of both worlds.
Jim