BT 5.0 transfer to BT 4.0

If i have a BT 5.0 beacon that sends 248 bytes instead of the 32 bytes sent by BT 4.0,
would a smartphone with BT be able to capture the whole 248 bytes? or would it have to
be a BT 5.0 smartphone?

If you want to send extended advertisements (available in BT 5) then you will need BT5 compliant device to receive it.
If want to send longer packets during connection then BT4.2 supported longer PDUs (up to 251 bytes).
Remember that a lot of features in Bluetooth are optional and this means that even if device claims to support Bluetooth version X some features might be not implemented.

How can I sand longer PDUs under the iBeacon protocol?
Where do I put the additional data?

iBeacon is not a protocol, but rather a packet format that is advertised though the air. It has a fixed length and it does not use Advertising Extensions (advertisement length of 255b) by specification.
Long PDU extension is for connections only and does not work for advertised packets like iBeacon.