Solder mask custom shape in altium
With your PCBdoc open, go to 


Place-->Solid Fill Region
Draw your custom shape
Double click on it to open up its properties
Set Kind: Copper, Layer: Top Solder (or Bottom Solder)


It might be easier to tin first, and then solder because then your components won't get in the way (you'll have hand/arm mobility). But if you can do it either way, then it doesn't matter, so no it won't have any adverse effects on your board.