The city of Kilkenny, which had become the capital of the Confederacy, was favourably placed for the direction of the war in Leinster and Munster. Nearly equidistant from Dublin, Cork, and Limerick, a meeting place for most of the southern and south-western roads, important in itself both as a place of trade, and as the residence of the Duke of Ormond and the Bishop of Ossory, a better choice could not, perhaps, have been made, so far as regarded the ancient southern "Half-Kingdom." But it seems rather surprising that the difficulty of directing the war in the North and North-West, from a point so far south, did not occur to the statesmen of the Confederacy. In the defective communications of those days, especially during a war, partaking even partially of the character of civil strife, it was hard, if not impossible to expect, that a supervision could be exercised over a general or an army on the Erne or the Bann, which might be quite possible and proper on the Suir or the Shannon. A similar necessity in England necessitated the creation of the Presidency of the North, with its council and head-quarters in the city of York; nor need we be surprised to find that, from the first, the Confederate movements combined themselves into two groups - the northern and the southern - those which revolved round the centre of Kilkenny, and those which took their law from the head-quarters of Owen O'Neil, at Belturbet, or wherever else his camp happened to be situated.
The General Assembly met, according to agreement, on the 23rd of October, 1642, at Kilkenny. Eleven-bishops and fourteen lay lords represented the Irish peerage; two hundred and twenty-six commoners, the large majority of the constituencies. Both bodies sat in the same chamber, divided only by a raised dais. The celebrated lawyer, Patrick Darcy, a member of the Commons' House, was chosen as chancellor, and everything was conducted with the gravity and deliberation befitting so venerable an Assembly, and so great an occasion. The business most pressing, and most delicate, was felt to be the consideration of a form of supreme executive government. The committee on this subject, who reported after the interval of a week, was composed of Lords Gormanstown and Castlehaven, Sir Phelim O'Neil, Sir Richard Belling, and Mr. Darcy. A "Supreme Council" of six members for each province was recommended, approved, and elected. The Archbishops of Armagh, Dublin, and Tuam, the Bishops of Down and of Clonfert, the Lords Gormanstown, Mountgarrett, Roche, and Mayo, with fifteen of the most eminent commoners, composed this council. It was provided that the vote of two-thirds should be necessary to any act affecting the basis of the Confederacy, but a quorum of nine was sufficient for the transaction of ordinary business. A guard of honour of 500 foot and 200 horse was allowed for their greater security. The venerable Mountgarrett, the head of the Catholic Butlers, (son-in-law of the illustrious Tyrone, who, in the last years of Elizabeth, had devoted his youthful sword to the same good cause,) was elected president of this, council; and Sir Richard Belling, a lawyer, and a man of letters, the continuator of Sir Philip Sydney's Arcadia, was appointed secretary.
The first act of this Supreme Council was to appoint General O'Neil as Commander-in-Chief in Ulster; General Preston, in Leinster; General Barry, in Munster; and Sir John Burke as Lieutenant-General in Connaught; the supreme command in the West being held over for Clanrickarde, who, it was still hoped, might be led or driven into the Confederacy. We shall endeavour to indicate in turn the operations of these commanders, thus chosen or confirmed; leaving the civil and diplomatic business transacted by the General Assembly, or delegated to the Supreme Council, for future mention.
Contrary to the custom of that age, the Confederate troops were not withdrawn into winter quarters. In November, General Preston, at the head of 6,000 foot and 600 horse, encountered Monk at Tymahoe and Ballinakil, with some loss; but before the close of December he had reduced Birr, Banagher, Burris, and Fort Falkland, and found himself master of King's county, from the Shannon to the Barrow. In February, however, he sustained a serious check at Rathconnell, in endeavouring to intercept the retreat of the English troops from Connaught, under the command of Lord Ranelagh, and the younger Coote; and in March, equal ill success attended his attempt to intercept Ormond, in his retreat from the unsuccessful siege of the town of Ross. Lord Castlehaven, who was Preston's second in command, attributes both these reverses to the impetuosity of the general, whose imprudence seems to have been almost as great as his activity was conspicuous. In April and May, Preston and Castlehaven took several strongholds in Carlow, Kildare, and West-Meath, and the General Assembly, which met for its second session, on the 20th of May, 1643, at Kilkenny, had, on the whole, good grounds to be satisfied with the success of the war in Leinster.
In the Southern Province, considerable military successes might also be claimed by the Confederates. The Munster troops, under Purcell, the second in command, a capable soldier, who had learned the art of war in the armies of the German Empire, relieved Ross, when besieged by Ormond; General Barry had successfully repulsed an attack on his head-quarters, the famous old Desmond town of Killmallock. In June, Barry, Purcell, and Castlehaven drove the enemy before them across the Funcheon, and at Kilworth brought their main body, under Sir Charles Vavasour, to action. Vavasour's force was badly beaten, himself captured, with his cannon and colours, and many of his officers and men. Inchiquin, who had endeavoured to form a junction with Vavasour, escaped to one of the few remaining garrisons open to him - probably Youghal.