They are auxiliary glyphs (輔助字形).
For example,

According to the wikibooks the rules to input them are as follows.
倉頡字母單獨成字時,取一碼即可。
The basic glyph (radical) that forms a word just takes ONE code.
For example, 日 is input with the key "A".
輔助字形單獨成字時,則須依拆碼規則拆碼。
An auxiliary glyph that forms a word should be decomposed according to the rules of decomposition.
For example, ⺜ is split into 冂(B), 一(M) and 一(M).
However, there are two more requirements in order to input them.
It is coded in Unicode.
(otherwise you have to make your own fonts)
The input method engine you use includes it.
(or you can make your own table)
For example,
⺜, ⺝ and 冃 are encoded and can be input with the keys BMM.
must be decomposed into 囗(W) and 丨(L).
Since it is not encoded, it cannot be input directly.