Well I am using sergbutos folowing mods...
1. Two extra merchants
2. Southampton class cruiser
3. Two Floatplanes mod
And as far as I know non of the above merchants will appear in convoys nor the cruiser in Task Forces.You would need to edit the RND layer file in the campaign folder and add them to the convoys/Task Forces yourself for them to appear with them I believe.
However I have had them appear as individual ships in the game though.
So for the most part your fears are unfounded..and it is pretty straightforward install of them.Though to get the Southamptn Cruiser to work you have to install the floatplanes mod also I think.
And none of the above ships replace any stock vessels in the game but simply add two more to the list.The floatplanes do not replace anything either as far as I know.
edit: EGADS!!!! How many more posts before I can get rid of this gay looking avatar