I'm a bit unclear on what you've done, but when you say I'm not looking for them to auto populate at this stage does that mean that you don't currently have an opentype liga feature which inserts these glyphs?
If not, and you're using the glyph palette to insert these, some applications (not sure about illustrator) will use the GID (glyph ID) to reference glyphs with no unicode value. If this is the case, you won't be able to change weights and preserve the glyphs unless the different weights contain the exact same glyph complement in the exact same order.
You really want to enter these ligatures as sequences of two (or more) characters and then let the liga or dlig features convert them to ligatures.
André