This is the second in a series of papers devoted to the study of a sample of 28 blue compact dwarf galaxies (BCDs). In the first paper, we presented the broadband observations in B, V, R, and I. Deep contour maps, surface-brightness profiles, and color profiles were used to analyze and discuss their morphology and structure. Here, we present new U-band and Hα observations. We compute isophotal and asymptotic magnitudes of the sample galaxies and total Hα fluxes. Comparison with previous works is done to assess the quality of the data available for BCDs. Finally, we produce an atlas of detailed color and Hα maps, the first systematic atlas of this kind published so far. The high quality of the data allows us to identify the different star-forming knots in the maps and to discriminate between them and the regions where star formation activity has already ceased. We supplement the atlas with a morphological description of each galaxy and group the galaxies in four classes according to the distribution of their star-forming regions.