These two are related. It kind of surprised me at the start too, that Chongkiat didn't break things down according to the principles of calligraphy. Pretty counterintuitive.1. Firstly, getting it out of my head that the 倉頡 Chong Kiat components are not necessarily (and in most cases, are not) the 康熙 traditional radicals themselves.
2. Applying the rule of maximum inclusion, i.e. identifying as large a chunk within the character as possible.
I think I know what U mean. Some characters break down right-left, top-bottom, or both. Other hanji are treated as one unit, where the Chongkiat code is usually the first three elements plus that last. It can be hard to tell beforehand which it's gonna be. Sometimes U just have to try both and see what works!3. When the character starts getting complicated, when I can apply the skipping rule, i.e. identify the key first couple of blocks, and then jump to the last one (in order to stay within the constraint of maximum 5 alphabets per character code).
Another thing to keep in mind is that different editions of Chongkiat have different codes for a few handfuls of hanji. The most expanded version of Chongkiat that I've seen takes in all versions.
U'll probably do great once U get issues #1 and #2 out of the way. Learning Chongkiat is kind of like learning how to write hanji. Everything adds up.4. In general, being creative with breaking the characters down and 'seeing' the blocks.
U might want to try typing up part of the 三字経 or some other writing and see which characters have U stumped.