while drawing chemical structures(in my case using software tool) say a molecule has a group x.the group x also has a bond indicative of the where the structure should be joined.
my question is when I substitute the group x in the main molecule do I include tat bond also?
thanks!

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while drawing chemical structures, say a molecule has a group x. The group x also has a bond indicative of the where the structure should be joined. My question is when I substitute the group x in the main molecule do I include that bond also?

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If I understand your question correctly, I believe the answer is "yes".

If you have a bond, C-H for example, and you substitute a Cl for an H, you would write or draw C-Cl with a line to show the chemical bond.

The only case where you might not draw the chemical bond is when drawing hydrocarbons (organic compounds). The C-H bond is often implicit, but I don't know how that relates to your drawing structure program.