Yes, you need to pay for the draft player, but the sum was mentioned after you've picked him.
i know that this is not the normal way, like in us sports or hockey in general. But the transfer fees are necessary in this kind of an online game, otherwise everyone would be able to sign players for free, or i need to code some contract negotiations (there is actually a discussion and a request to add something like this for free agents).
But you can train rookies by yourself, just build the youth development to level 1 (in the training section). Rookies with a maximum strength of 15 are free to train. You can train better rookies, too. In that case you must pay a daily amount and/or upgrade the development center.
To gain more money you should expand your stadium and your stadium environment you can play friendly games, too.