It is fine to practice both types of transmutation at different parts of the day. What might prove counterproductive, although some might argue with me, is to practice two different types of transmutation during the same practice. I'd advise you work with one transmutation practice for one session so that you remain concentrated and reap the most benefit from the exercise, rather than trying too many things at once. Other than that, it is perfectly fine to practice, say, Ham-Sah in the morning and Egyptian Christic Pranayama in the evening.

Pranayama develops the faculties of imagination. Therefore, even if your imagination is weak in the beginning, the exercise of sexual transmutation will fortify the chakras immensely, especially the Chakra Ajna (Church of Philadelphia), in order to harmoniously and slowly develop the capacities for visualization. Practice makes perfect.