mine where siliconed in also, the best way for me was to use a pair of needle nose pliers ,grab one end of the left over silicon and sort of roll it up around the pliers worked really good,the new boots are different,they don't have the extra rim that seats in the control arm,which is fine for the top a-arm but the bottom will form a dam around the new ball joint that will eventually fill with water,dirt,so I just filled the void with some more silicon.
old on the left,new on the right
you can also make your own make shift press to remove the old ball joints these are some concret anchors I had ,but you could use some all thread.
