There is a hack floating around (I can't find it yet) to replace your 1 Meg Agnus with a 2 Meg Super Agnus (the one used in the A3000). IIRC, the 4 existing ram chips are pulled and 8 new 1Meg chips are installed. With just a few trace mods you get 2 Megs of chip on the motherboard. You must then disable the memory on the A501 but you can still use the clock. I did this modification almost 15 years ago and that machine is still running strong.
BTW: I thought I saw 2 meg Agnus for sell on AmigaKit.
If you have 1 Meg of chip (512K on the mb and 512K on the A501), whats the advantage of moving it all to the mb? You still need the RTC. If you add another 512K (1.5 meg total) with some kind of glue logic, that 512K wont be true chip nor true fast memory.
You probably know this, but Supra's 500 RX fast ram expansion is one of the best first moves you can make (if you're not going for a HD/ram combo). I wish I had had one of these back in 1989!