Patching up really isnt enough m8 and will kick you in the a*se somewhere along the line..............
Really take out the base and do the job properly either the tuff2 or tilux bases can be cut no problem which will then give you a secure job when tanked.
If not then you have to secure the transitions between the floor+upstand, upstand+wanabe tray and if your working with wood it wont be easy. If you want to go this way then say so and I will sort you. (It can be waterproofed but there will always be a risk of transition cracks in the tiling)
cheers
tiler