The use of filter banks for implementing multicarrier spread spectrum systems leads to a class of effective waveforms that are highly resilient to partial-band interferers. Such waveforms can be also designed to keep the peak-to-average power ratio (PAPR) of the resulting signal at a minimum level. The use of multiple spreading gain vectors (known as multicodes), on the other hand, is an effective method for increasing the data rate in spread spectrum systems, in general. This paper presents a detailed analysis of a class of filter bank multicarrier spread spectrum (FBMC-SS) waveforms and demonstrates an effective receiver implementation of them when multicodes are applied. Application of the developed multicode waveform for communications over high-frequency (HF) skywave channels is also explored, and the benefits that it provides are studied both numerically, through computer simulations, and experimentally, by examining the receivers performance over a variety of skywave links.